Israel and Iran Claim Victory as Cease-Fire Takes Hold

The report’s finding, while preliminary, was particularly damaging because it emerged from inside the Pentagon, which had carried out the strikes, and it concluded that the military action had only set Iran’s nuclear program back by a number of months.

Mr. Trump had been eager to celebrate his success at NATO and revel in the fact that he had conducted an attack that none of his predecessors had dared to launch. His view was backed up by Mark Rutte, the secretary general of the alliance, who wrote Mr. Trump a private message thanking him for his “decisive action” in Iran.

“That was truly extraordinary, and something no one else dared to do,” Mr. Rutte wrote. “It makes us all safer.” The note, addressed to “Donald,” appeared to be a private correspondence, but Mr. Trump posted a photo of it on his social media account.

Mr. Rutte went on to tell Mr. Trump that he was “flying into another big success in The Hague this evening,” citing the alliance’s agreement that each nation would spend 5 percent of its gross domestic product on defense or defense-related spending, though they have a decade to reach the mark.

That is a major victory for Mr. Trump, who has pressed for the past decade for Europe to pay for more of its own defense. While the commitments increased under the Biden administration, Mr. Rutte has leveraged the concerns about Russia’s ambitions beyond Ukraine to convince countries to spend at levels that even six months ago they could not have imagined. And Mr. Trump’s unsubtle threats in his first term that he might abandon the alliance proved successful, even if they came at the price of diplomatic breaches with some of America’s closest allies.

By any measure, Mr. Trump’s actions in the past 72 hours underscored to those countries, however, how advanced the U.S. military was compared to the other forces that make up NATO. No other nation represented in the alliance has a military capable of flying halfway around the world to strike a distant, hardened target under a mountain in north-central Iran.

But the subtext of the meeting that opened in The Hague on Tuesday evening was clear: The other 31 NATO nations must adjust to an era in which they can no longer count on Washington as the linchpin of the 76-year-old alliance. The biggest source of tension at the session is Mr. Trump’s unwillingness to commit more military aid to Ukraine, and his frequent communications with President Vladimir V. Putin of Russia make the allies nervous.

Mr. Trump woke up on Tuesday morning in a surly mood, as the cease-fire between Israel and Iran he had just eagerly announced hours before appeared to be collapsing. As he was leaving the White House, he berated Israel and Iran, saying they “don’t know what the fuck they’re doing” as the two sides launched missiles as the truce was set to begin.

Mr. Trump then called Mr. Netanyahu and later announced the cease-fire was back in place. He was in a much better mood then, posting a series of laudatory messages from others, including calls for him to win the Nobel Peace Prize.

The upbeat demeanor crumbled once the intelligence reports started to leak out, with Karoline Leavitt, the White House press secretary, blasting the findings as “flat-out wrong” and a “clear attempt to demean President Trump.”

Later that night, Mr. Trump appeared to dig in, posting on social media a series of quotes from administration officials, as well as the front page of one newspaper, using the word “obliterated” to describe the damage.

“Our bombing campaign obliterated Iran’s ability to create nuclear weapons,” Defense Secretary Pete Hegseth told CNN on Sunday, in one passage Mr. Trump posted. “Our massive bombs hit exactly the right spot at each target and worked perfectly.”

At The Hague, the president will face an alliance that he has long disdained in a setting — an international summit — that he has shown little interest in. For that reason, Mr. Rutte bent over backward to try and appease Mr. Trump. Mr. Rutte shortened the programming, corralled the alliance to meet Mr. Trump’s spending demand and worked to keep the policy communiqué as short as five paragraphs.

In total, Mr. Trump is expected to spend less than 24 hours on the ground in the Netherlands. He attended a dinner with other world leaders on Tuesday night and spent the night at Huis ten Bosch, one of the Dutch royal palaces. He will have breakfast with the country’s king and queen on Wednesday morning and then participate in the plenary session and hold bilateral meetings and a news conference before returning to Washington.

Even before he arrived, though, Mr. Trump further unnerved European allies, playing coy on whether he was committed to Article 5, the part of NATO’s treaty that stipulates an attack on one ally would be defended as an attack on all. During his first term, Mr. Trump edited out mentions of Article 5 from a major speech at NATO. On Tuesday, the president said his commitment “depends on your definition” of Article 5.

“I’m committed to saving lives,” he said. “I’m committed to life and safety, and I’m going to give you an exact definition when I get there. I just don’t want to do it on the back of an airplane.”

“Today, following your courageous resistance, this great and history-making nation witnesses a cease-fire and the end of a 12-day war that was imposed on the Iranian people, through the recklessness and belligerence of the Zionist regime,” he said in a written message published by IRNA, the state news agency.

In a war where all parties are claiming victory, the Iranian president’s comments stood in stark contrast to assertions made by leaders in the United States and Israel about the impact of attacks. Mr. Pezeshkian’s claim of victory came as leaders in Israel and the United States were contending that their strikes had successfully thwarted Iran’s ability to build a nuclear weapon.

Mr. Trump has claimed that three of Iran’s nuclear facilities were “completely and totally obliterated” by American strikes over the weekend, even as other U.S. officials offered more cautious assessments of the damage. On Tuesday, Mr. Trump said, “It was my great honor to Destroy All Nuclear facilities & capability, and then, STOP THE WAR!”

A preliminary classified U.S. report on Tuesday cast doubt on those claims.

Israel has also targeted Iranian nuclear facilities, as well as Iranian scientists, killing at least 14 by its account. It has also killed top Iranian military leaders.

On Tuesday, Prime Minister Benjamin Netanyahu said that Israel had “achieved all the goals” of its campaign in Iran and more, including removing the “immediate” threat of it developing nuclear weapons and the threat to Israeli security from Iranian ballistic missiles.

The Iranian president said in his statement to the nation that the loss of “women, children, scientists, and brave military commanders,” as well as damage to some infrastructure, had dealt a “grave blow” to the country. Iran’s health ministry said on Tuesday that the death toll from the Israeli strikes had surpassed 600 people.

But Mr. Pezeshkian insisted that the losses Iran had inflicted on Israel “have been beyond imagination,” blaming “a heavy media and propaganda blackout” for any indications otherwise. The Magen David Adom emergency service in Israel said on Tuesday that 28 people had died in Iranian strikes since the war’s start earlier this month.

Mr. Pezeshkian said that Iran had sent a “powerful message to the world” with its attacks on Israel, eroding “the myth of the Zionist regime’s invincibility” by causing “wide-scale destruction to vital centers” and infrastructure. The Iranian response showed “the cost of adventurism against the great nation of Iran is tremendously high,” he said.

Mr. Pezeshkian said that Iran had been in the midst of “diplomatic efforts to resolve misunderstandings through negotiations” when Israel initiated its attacks, an apparent reference to talks with the United States over its nuclear program. Those talks stopped when Israel attacked and the United States joined the conflict about one week later.

“History will remember the betrayals and broken promises of Iran’s enemies,” Mr. Pezeshkian said.

Separately, in a phone call with the leader of the United Arab Emirates, Sheikh Mohammad bin Zayed, Mr. Pezeshkian signaled a willingness to return to talks, saying Iran was “ready to resolve issues at the negotiating table and within international frameworks,” according to an official readout of the call by the president’s office.

He also asked the Emirati leader to convey to the United States that Iran was “simply seeking its legitimate rights and has no demands beyond this, and definitely has not and will not seek a nuclear weapon.”

Mr. Pezeshkian, in his message to Iranians, also sought to reassure neighbors in the Middle East that Iran is keen on peace. “We have a deep belief in coexistence and stability,” he said. “The power and defensive capabilities of the Islamic Republic of Iran have always served peace and friendship among Muslim brothers and historical neighbors and will continue to do so.”

Above all else, the Iranian president’s address emphasized the cohesion of the Iranian people during the war, calling them “the nation’s greatest assets.”

He thanked them for their endurance and resilience, and said the government would work to compensate those who experienced losses. “Starting today,” he said, “we will work toward a better tomorrow, a brighter future and a stronger Iran — together and side by side.”

The briefings were to have included top White House and intelligence officials, including Tulsi Gabbard, the director of national intelligence; John Ratcliffe, the C.I.A. director; and Gen. Dan Caine, chairman of the Joint Chiefs of Staff.

The Senate briefing has been rescheduled for Thursday, according to one person familiar with the situation who spoke on the condition of anonymity because they were not authorized to comment on it. Speaker Mike Johnson said the House briefing had been moved to Friday.

The delay came as a preliminary classified U.S. report suggested that the bombing of Iran’s nuclear sites did less damage than the “obliteration” that Mr. Trump has claimed, sealing off the entrances to two of the facilities but not collapsing their underground buildings, according to officials familiar with the findings.

It also followed a newly reached cease-fire brokered by Mr. Trump between Iran and Israel, which he announced before he and senior national security officials left Washington early Tuesday for the annual NATO summit in the Netherlands.

Several senior Democrats have pushed the administration to fulfill its legal obligations under the War Powers Resolution of 1973, which requires the president to notify Congress within 48 hours of military action and to provide a classified briefing. On Monday evening, Mr. Trump sent a short memo to lawmakers asserting that the strikes had been carried out under his constitutional authority “to protect United States citizens both at home and abroad as well as in furtherance of United States national security and foreign policy interests.”

The Senate minority leader, Chuck Schumer, Democrat of New York, sharply criticized the delay.

“This last-minute postponement of our briefing is outrageous, it’s evasive, it’s derelict,” he said at a news conference on Tuesday. “There is a legal obligation for the administration to inform Congress about precisely what is happening.”

Mr. Johnson, who has been quick to cede congressional power since Mr. Trump took office, said he had no problem with the delay. The “tentative plan,” he said, was for Defense Secretary Pete Hegseth and Marco Rubio, who is serving as both secretary of state and the national security adviser, to brief lawmakers as soon as they were available.

“The White House and the executive branch, and both of those secretaries I named, have utmost respect for our Article One authority and our chambers here, and they want the House and Senate to have all the information, and so they’re going to deliver it as soon as possible,” Mr. Johnson told reporters, referring to the part of the Constitution that gives Congress the power to declare war. “And I think that’s satisfactory to me, and it should be to all my colleagues.”

The classified briefing is seen by some lawmakers as central to the debate on Capitol Hill over Congress’s role in authorizing offensive military action. While most Republicans have backed the strikes and deferred to Mr. Trump’s judgment, consistent with their posture toward the president since his return to office in January, many Democrats have argued that deploying multiple B-2 bombers with 30,000-pound bombs to Iran without consulting Congress is a violation of the Constitution’s separation of powers.

Before the president’s memo was sent, Representative Hakeem Jeffries, the House minority leader, described the strikes as “offensive,” apparently working to pre-empt an argument from the White House that the strike had been a matter of self-defense.

“The use of military force which is offensive in nature must be approved by the House and the Senate,” Mr. Jeffries said during a news conference on Monday. “It’s not optional, Donald. It’s not.”

Mr. Jeffries said lawmakers had seen “no evidence to date” that the strikes were legally justified or that an “imminent threat” to the United States existed. “If the administration has evidence to the contrary, come up to present it,” he said.

Monday’s memo from Mr. Trump said the action was taken in part for the “collective self-defense of our ally, Israel,” but gave no additional details.

Catie Edmondson contributed reporting.

Although both countries presented competing versions of the night’s events, their explanations — and quiet skies over both countries as night fell Tuesday — suggested that they both wanted the cease-fire to hold. Here is what we know about what unfolded overnight.

Before the attack, U.S. intelligence agencies had said that if Iran tried to rush to making a bomb, it would take about three months. After the U.S. bombing run and days of attacks by the Israeli Air Force, the report by the Defense Intelligence Agency estimated that the program had been delayed, but by less than six months.

The report also said that much of Iran’s stockpile of enriched uranium was moved before the strikes, which destroyed little of the nuclear material. Iran may have moved some of that to secret locations.

Some Israeli officials said they also believed that the Iranian government had maintained small covert enrichment facilities so it could continue its nuclear program in the event of an attack on the larger facilities.

Other officials noted that the report found that the three nuclear sites — Fordo, Natanz and Isfahan — had suffered moderate to severe damage, with the facility at Natanz damaged the most. It is not clear whether the Iranians will try to rebuild the programs.

Former officials said that if Iran tried to quickly develop a bomb, it would be a relatively small and crude device. A miniaturized warhead would be far more difficult to produce, and the extent of damage to that more advanced research is not clear.

Current and former military officials had cautioned before the strike that any effort to destroy the Fordo facility, which is buried more than 250 feet under a mountain, would probably require waves of airstrikes, with days or even weeks of pounding the same spots.

American warplanes did hit the same spots at least twice on Saturday. B-2s dropped 12 GBU-57 Massive Ordnance Penetrator bombs — often referred to as “bunker busters” — on Fordo, and six aboveground entry craters are now visible, according to Brian Carter, the Middle East portfolio manager at the American Enterprise Institute.

But many military bomb experts believed that more than one day of strikes would be needed to complete the job.

The initial damage assessment suggests that President Trump’s claim that Iran’s nuclear facilities were “obliterated” was overstated. Congress had been set to be briefed on the strike on Tuesday, and lawmakers were expected to ask about the findings, but the session was postponed. Senators are now set be briefed on Thursday, and House members on Friday.

Since the strikes, Mr. Trump has complained to advisers repeatedly about news reports that have questioned how much damage was done, said people with knowledge of the comments. He has also closely watched the public statements of other officials when they are asked about the damage to the nuclear facilities, they said.

In a statement on Tuesday, Defense Secretary Pete Hegseth reiterated Mr. Trump’s early assessment.

“Based on everything we have seen — and I’ve seen it all — our bombing campaign obliterated Iran’s ability to create nuclear weapons,” he said. “Our massive bombs hit exactly the right spot at each target and worked perfectly.”

Officials cautioned that the five-page classified report was only an initial assessment, and that others would follow as more information was collected and as Iran examined the three sites. One official said that the reports people in the administration had been shown were “mixed” but that more assessments were yet to be done.

But the Defense Intelligence Agency report indicates that the sites were not damaged as much as some administration officials had hoped, and that Iran retains control of almost all of its nuclear material, meaning if it decides to make a nuclear weapon it might still be able to do so relatively quickly.

Officials interviewed for this article spoke on the condition of anonymity because the findings of the report remain classified.

The White House took issue with the assessment. Karoline Leavitt, a White House spokeswoman, said its findings were “flat-out wrong.”

“The leaking of this alleged assessment is a clear attempt to demean President Trump, and discredit the brave fighter pilots who conducted a perfectly executed mission to obliterate Iran’s nuclear program,” she said in a statement. “Everyone knows what happens when you drop 14 30,000-pound bombs perfectly on their targets: total obliteration.”

Elements of the intelligence report were reported earlier by CNN.

The strikes badly damaged the electrical system at Fordo, officials said. It is not clear how long it will take Iran to gain access to the underground buildings, repair the electrical systems and reinstall equipment that was moved.

There is no question that the bombing campaign “badly, badly damaged” the three sites, Mr. Carter said.

But initial Israeli damage assessments have also raised questions about the effectiveness of the strikes. Israeli defense officials said they had also collected evidence that the underground facilities at Fordo were not destroyed.

Before the strike, the U.S. military gave officials a range of possibilities for how much the attack could set back the Iranian program. Those ranged from a few months on the low end to years on the higher end.

Some officials cautioned that such estimates are imprecise, and that it is impossible to know how long Iran would exactly take to rebuild, if it chose to do so.

Despite claims of the sites’ obliteration by Mr. Trump and Mr. Hegseth, Gen. Dan Caine, the chairman of the Joint Chiefs of Staff, has been more careful in describing the attack’s effects.

“This operation was designed to severely degrade Iran’s nuclear weapons infrastructure,” General Caine said that at the Sunday news conference.

The final battle damage assessment for the military operation against Iran, General Caine said on Sunday, standing next to Mr. Hegseth, was still to come. He said the initial assessment showed that all three sites “sustained severe damage and destruction.”

General Caine added that it was “way too early” to assess how much of Iran’s nuclear program remained.

Gen. Joseph L. Votel, the former commander of Central Command, said in an interview, that he had “a lot of confidence in the weapons systems used.” But he added: “I’m not surprised that elements survived. That’s why you do battle damage assessments, because everything can go as planned but there are still other factors.”

At a Senate hearing on Tuesday, Democrats also struck a more cautionary note.

“We still await final battle damage assessments,” said Senator Jack Reed of Rhode Island, the senior Democrat on the Armed Services Committee.

Military officials had said that to do more significant damage to the underground sites, they would have to be hit with multiple strikes. But Mr. Trump announced he would stop the strikes after approving the first wave.

U.S. intelligence agencies had concluded before the strikes that Iran had not made the decision to make a nuclear weapon, but possessed enough enriched uranium that if it decided to make a bomb, it could do so relatively quickly.

While intelligence officials had predicted that a strike on Fordo or other nuclear facilities by the United States could prompt Iran to make a bomb, U.S. officials said they do not know yet if Iran would do so.

Representatives of the Defense Intelligence Agency did not respond to requests for comment.

David E. Sanger contributed reporting.

Mr. Kaine and two other Democratic backers of the resolution, Senators Adam Schiff of California and Andy Kim of New Jersey, introduced language on Tuesday specifying that the curb would only apply to offensive action, not for the United States’ continuing support for Israel “in taking defensive measures” against Iran or its proxies.

The amendment also would make explicit that congressional authorization would not be needed to defend against attacks on American personnel or facilities abroad or for the United States to continue sharing intelligence with allies like Israel in response to Iranian threats.

Mr. Schiff said in a statement that the changes were meant to clarify that the resolution would “not limit our ability to protect our troops or aid Israel in its own defense, should Iran continue to engage in attacks against us and our allies.”

The resolution stands little chance of approval. With Republicans holding majorities in both chambers of Congress, it is unlikely that any measure restricting Mr. Trump’s military authority will succeed. But by putting it forward, Mr. Kaine and other lawmakers who back such measures have reinvigorated a long-dormant debate over Congress’s role in matters of war.

The changes may make Mr. Kaine’s measure more palatable for some Democrats who are concerned that Mr. Trump did not seek Congress’s approval before authorizing the bombings yet are reluctant to embrace any legislation that could tie the president’s hands in backing Israel.

Democrats have been deeply divided over backing Israel, with some in the party strongly supportive but many on the left deeply opposed to doing so. But since the strike, they have sought to find common ground in their outrage that Mr. Trump neither sought authorization nor consulted with Congress before moving against Iran, and the modifications appeared designed to foster as much unity as possible.

On Tuesday, Senator Chuck Schumer, Democrat of New York and the minority leader, excoriated the Trump administration for canceling a classified briefing with lawmakers that had been scheduled to brief them on the strike.

“What is the administration so afraid of?” Mr. Schumer said in a statement. “Why won’t they engage with Congress on the critical details: the results of the recent strike, the scope and trajectory of this conflict, the administration’s long-term strategy to prevent Iran from obtaining nuclear weapons, and the potential risks facing American citizens and our service members?

In the House, three top national security Democrats, Representatives Jim Himes, Gregory Meeks and Adam Smith, introduced a separate War Powers Resolution late on Monday that also seeks to invoke congressional authority over the use of U.S. forces in the Middle East.

That measure also includes language that would reaffirm self-defense priorities and make clear that their aim is not to limit executive authority when responding to attacks on either U.S. interests or American allies, including Israel.

“The War Powers Resolution we’ve introduced today orders the removal of U.S. Armed Forces from hostilities against Iran, while allowing U.S. forces to carry out defensive operations to defend the United States and its partners and allies from imminent attack, including those defending Israel,” the three — the senior Democrats on the Intelligence, Foreign Affairs and Armed Services Committees — said in a joint statement.

Leading Republicans, and even some anti-interventionist members of the party, have refused to consider limiting Mr. Trump’s war-making authority, saying he exercised his presidential power appropriately in striking Iran. Speaker Mike Johnson said on Tuesday that he believed the War Powers Act, the 1973 law that requires congressional authorization for the use of military force, is unconstitutional.

And some Democrats are equally opposed.

“I don’t want any mission creep,” said Senator John Fetterman of Pennsylvania, a vocal supporter of Israel who has celebrated the Iran strike. He said congressional intervention was not needed until a “full-on war” started and said involving lawmakers would have hampered the operation against Iran.

A parallel bipartisan effort is also underway in the House led by Representatives Thomas Massie, Republican of Kentucky, and Ro Khanna, Democrat of California. But late Monday, after Iran launched missiles at the largest U.S. military base in the Middle East and Mr. Trump claimed on social media that Israel and Iran had agreed to a cease-fire, its Republican sponsor suggested he might not push for a vote.

“If a cease-fire holds, the resolution becomes a moot point,” Mr. Massie told reporters on Monday. “I wouldn’t need to bring it to the floor.”

Mr. Khanna said he and Mr. Massie were “taking a wait-and-see approach about whether a vote will be needed now on our War Powers Resolution.”

The intercepted Iranian attack also briefly interrupted air traffic in Bahrain, Kuwait and the United Arab Emirates, the home of Dubai International Airport, the second-busiest airport in the world. The airspace closure there was short enough that disruptions appeared to be minimal.

About 1,000 flights — with a total of about 359,000 seats — were scheduled to depart from North America to Doha and Dubai this month before the cancellations, according to Cirium. Qatar Airways alone had an average of 5,500 total daily seats on flights from North America in June.

In addition to the cancellations, at least 85 flights to Doha, Dubai and Abu Dhabi were diverted on Monday, according to Cirium.

On social media, hundreds of users posted messages asking airlines if their flights to or from the Middle East were operating as scheduled, as passengers heard conflicting messages about cancellations.

Reima Abu was booked on a Qatar Airways flight from Chicago to Doha on Tuesday but was unsure if she would be able to fly after an airline representative told her by phone that her flight had been canceled, but then she read on social media that it had been reinstated. Ms. Abu, 23, planned to visit family in Jordan, but her connecting flight on another airline was canceled. She was also worried about safety.

“Factors like, is it actually safe or will another country attack is on my mind,” she said via text message.

Linda Gradstein of Jerusalem, who was returning home from New Zealand via Doha on Tuesday, said in a voice message that her flight had been diverted to Oman, where it spent five and a half hours on the tarmac before flying on to Qatar. Once passengers arrived in Doha, she said, there was “complete chaos” at the airport, with travelers crowding the transfer desk. “People were pushing, people got punched,” she said, adding that the airport staff tried to be helpful and handed out water.

Qatar Airways said it “is now making progress in restoring its schedule” but warned of possible disruptions until Thursday. The carrier is allowing passengers to change their travel dates without paying a fee for flights through June 30.

U.S. carriers including American Airlines and United Airlines have indefinitely suspended flights to Doha and Dubai, but those carriers make up a tiny fraction of traffic to the cities, which are primarily served by their national carriers.

Major U.S. airlines suspended flights to Ben Gurion Airport near Tel Aviv when Israel closed its airspace on June 13. That closure appeared to be easing on Tuesday as some airlines, including El Al, resumed limited flights. Iranian airspace appeared to still be closed on Tuesday night, according to Flightradar24.

Isabel Kershner contributed reporting.

The index now sits less than 1 percent away from its February record high, having staged a sharp recovery from April’s tariff-induced sell-off. The Trump administration has walked back many of its original trade proposals, spurring that recovery.

A second day of declining oil prices helped lift stocks. Energy costs are a primary expense for companies, making them an important factor in inflation calculations. Investors hope that reduced oil prices will help keep inflation trending lower.

Brent crude, the international benchmark, fell just over 6 percent on Tuesday after dropping more than 7 percent a day earlier, its biggest one-day decline in almost three years. West Texas Intermediate crude, the oil benchmark in the United States, also fell more than 6 percent, to $64.37 per barrel, on Tuesday.

Investors’ concerns about inflation appeared to ease alongside the drop in oil prices, which contributed to a dip in government bond yields. Analysts also pointed to congressional testimony from Jerome H. Powell, the chair of the Federal Reserve, which appeared to buoy investors’ hopes that interest rates could be lowered sooner than expected. The 10-year Treasury yield fell below 4.30 percent for the first time in over a month.

Elsewhere, markets also rallied. European and Asian stock indexes rose on Tuesday, after being more mixed on Monday.

Yet despite the discordant Iranian and Israeli claims about timelines, the mutual denials of violations strongly suggested that each side wanted the cease-fire to hold.

Prime Minister Benjamin Netanyahu of Israel said on Tuesday afternoon that the cease-fire had been set to take effect at 7 a.m. Israel time. Four hours earlier, at 3 a.m., Israel attacked targets “in the heart of Tehran,” his office said in a statement, adding that shortly before the truce came into effect Iran fired a barrage of missiles at Israel.

One hit an apartment building in the southern Israeli city of Beersheba, killing four people.

At 7:06 a.m. in Israel, Iran fired another missile, and then two more at 10:25 a.m., according to Israel. Mr. Netanyahu’s office said those missiles were intercepted or fell in open areas.

In response, Mr. Netanyahu’s office said, Israeli forces destroyed a radar position near Tehran.

By then, Mr. Trump had publicly demanded that Israel not respond, describing the last volley of missiles fired by Iran at northern Israel as “one rocket that didn’t land, that was shot perhaps by mistake.”

Despite earlier threats from the Israeli defense minister and military that Israel would respond forcefully to the missile fire, the actual Israeli response appeared to be limited and symbolic.

“Following a conversation between President Trump and Prime Minister Netanyahu, Israel refrained from further attacks,” the statement from Mr. Netanyahu’s office said.

Around the same time, Mr. Trump wrote on social media that Israel’s warplanes would “turn around and head home.”

Iran, for its part, said its missile fire came as retaliation for Israel’s pre-dawn bombardment, and only before the cease-fire was meant to start.

The Islamic Revolutionary Guards Corps said that in retaliation for “savage” Israeli attacks on Iran overnight, Iran had launched 14 missiles at military and logistical centers in Israel in the “final minutes” before the cease-fire came into effect, according to a statement published on the Telegram channel of Press TV, an Iranian state news channel. The statement made no mention of the firing any missiles after the cease-fire came into force, as Mr. Trump and Israel charged.

In addition, an Iranian military spokesman, Lt. Col. Ebrahim Zolfaqari, said Israel had launched “three waves of attacks” against Iran on Tuesday morning, after the cease-fire was supposed to take effect, with the last ending at 9 a.m. Iranian time, according to a Press TV report citing a report from Defa Press, another Iranian outlet.

Fars, a news agency managed by the Revolutionary Guards, reported that explosions were heard in Babol and Babolsar, Iranian cities to the northeast of Tehran, without providing a time or any other details.

Mr. Trump first announced that Israel and Iran had agreed to a cease-fire deal on Monday evening — around 1:30 a.m. Tuesday in Tehran — and Iran’s state television later announced a cease-fire early on Tuesday morning local time. The Israeli government remained silent until it made its own announcement of a cease-fire at about 9 a.m. Israel time, saying Israel had agreed to the truce.

As he departed Washington on Tuesday morning for a NATO summit in the Netherlands, Mr. Trump fumed about violations of the cease-fire he had heralded, saying that he “didn’t like the fact that Israel unloaded right after we made the deal.”

“They didn’t have to unload,” he said, “and I didn’t like the fact that the retaliation was very strong.”

Mr. Trump also said he was unhappy to learn that Israeli warplanes had headed out to retaliate for the Iranian missile fire hours after the truce came into effect.

“I think they both violated it,” he said. “I don’t think, I’m not sure they did it intentionally. They couldn’t rein people back.”

But it seems that Qatar had already begun to help to broker a truce, engaging quietly with Israel’s American allies and with the Iranian government behind the scenes.

“What happened shows Qatar can take a hit but be pragmatic,” said Sanam Vakil, the director of the Middle East and North Africa Program at Chatham House.

After the United States intervened on the side of Israel and bombed Iranian nuclear sites on Sunday morning, Iran responded by attacking the Al Udeid aid base in Qatar.

Qatar knew in advance that an attack on the base was planned on and almost all missiles fired at the site were intercepted, according to Maj. Gen. Shayeq Misfer al-Hajri, the Qatari deputy chief of staff for joint operations.

On Tuesday, the Qatari foreign ministry summoned the Iranian ambassador in Doha but did not announce any punitive measures against Iran.

The Qatari government’s swift shift from defending its right to respond to playing mediator suggested an element of “choreography,” said Nicholas Hopton, who was Britain’s ambassador to Qatar from 2013 to 2015.

As Qatar and the other Gulf nations watched the Israel-Iran war unfold over the past two weeks, they worried that an escalation could result in Iran targeting their strategic energy resources, undermining a critical source of their revenue.

If the Iranian government was set on targeting American soldiers in the Gulf, it may have viewed the base in Qatar as less likely to provoke an escalation or damage its relations with some other Gulf Arab countries, which had been warming in recent years.

The wealthy emirate of Qatar has generally maintained closer ties with Iran than most of the other Gulf countries. It has also played a leading role in mediating between Israel and Hamas, the Iran-backed Palestinian militant group, since the war in Gaza began in October 2023.

If Iran attacked another Gulf nation, it might have run into more complicated territory.

The headquarters of the U.S. Navy’s Fifth Fleet, in Bahrain, and Saudi Arabia’s oil installations could also have become targets. But Iran’s diplomatic relations with these two other Gulf nations are still new and relatively shaky.

The United Arab Emirates is one of Iran’s largest trading partners, offering Iran a vital link to the global economy as it navigates longstanding Western sanctions. The prospect of missiles flying over Dubai, a glitzy metropolis in the Emirates, would have alienated a neighbor that Iran depends on.

Qatari officials intervened with Iran on behalf of the Trump administration, according to three diplomats briefed on the matter, who spoke on the condition of anonymity to discuss sensitive diplomacy. They said that Mr. Trump had told the emir of Qatar, Sheikh Tamim bin Hamad al-Thani, that Israel had signed off on an American cease-fire proposal.

The president had asked Qatar to help bring Iran on board, the diplomats said. The Qatari prime minister, Sheikh Mohammed bin Abdulrahman al-Thani, then persuaded Iran to agree to the truce proposal by late Monday in a call with the Iranian leadership, the diplomats said.

A senior White House official, who requested anonymity because they were not authorized to discuss the negotiations publicly, said the Qatari emir played a role in the cease-fire discussions.

The truce took effect early Tuesday morning and appeared to be holding as evening approached.

Qatar’s handling of the crisis illustrated the value the wealthy Gulf emirate puts in its relationship with the United States, said Mr. Hopton, the former British diplomat.

“Trump wanted a de-escalation and Qatar was able to help him with that,” Mr. Hopton said.

A pillar of Qatar’s foreign policy is to maintain a close relationship with the United States, and Qatari officials frequently take advantage of opportunities to prove to the American government that they can be a strategic ally on important American foreign policy objectives.

With a small army, Qatar relies on the United States to provide it with a security blanket. Saudi Arabia and the United Arab Emirates, powerful neighboring countries, have occasionally taken hostile positions against Qatar.

Vivian Nereim and Maggie Haberman contributed reporting to this article.