The Food and Drug Administration’s top vaccine official rejected broad uses of two Covid vaccines, citing unknown risks or injuries despite assurances of safety from dozens of staff experts, newly released documents show.

The decisions by the official, Dr. Vinay Prasad, the agency’s new chief medical and scientific officer, stunned agency veterans. Records show that the F.D.A.’s vaccine staff members had signed off on approving the Novavax vaccine, an alternative to mRNA shots and weeks later on the next-generation of the mRNA Covid shot by Moderna for anyone 12 and older.

Dr. Prasad overruled those recommendations by the end of May and instead advised restricting the use of both Covid vaccines. He wrote in two memos that the threat from the virus had fallen and changed the risk-benefit balance of vaccinating healthy, younger people.

The changes for the two vaccines aligned with the agency’s broader plan that limited the use of all Covid vaccines to people 65 and older. For those younger than 65, the F.D.A. rolled back eligibility for Covid vaccines to those with a medical condition that would put them at high risk.

The new documents offer a window into Dr. Prasad’s vision for the agency and his thinking on vaccine policy. The records reveal that F.D.A. staff members concluded that the vaccines were safe and effective based on clinical trials of the shots tested in thousands of people. But Dr. Prasad wrote that there could still be vaccine-related injuries that have yet to be discovered.

“Even rare vaccination-related harms, both known and unknown, now have a higher chance of outweighing potential benefits in non-high-risk populations,” he wrote in the documents overriding the staff members on the Novavax shot.

His decisions were part of a broader F.D.A. reversal of years of Covid vaccine policy announced in May by Dr. Prasad and Dr. Marty Makary, the agency commissioner. The changes mean that doctors will have to write so-called off-label prescriptions for younger people who want protection from the virus, which experts said could be a barrier for some patients.

On the Moderna approval, Dr. Prasad filed a “center director override memo,” a document signed on rare instances when top officials substitute their decisions over the findings of staff experts.

Andrew Nixon, a spokesman for the Health and Human Services Department, disputed the account. “The idea that Dr. Prasad ‘overruled’ F.D.A. scientists is a distortion of the facts,” Mr. Nixon wrote in an email.

“He evaluated the totality of the evidence and made a judgment rooted in gold-standard science,” he said. “That’s not political — it’s what principled leadership looks like.”

Vaccine and infectious disease experts who reviewed the memos said that Dr. Prasad had failed to weigh the well-documented harmful effects from the coronavirus itself, including long Covid and other post-Covid lung, heart and blood-clotting problems. The F.D.A. staff members, in their records, had noted that long Covid “has been recognized as a significant and serious consequence” of contracting the virus.

“It is a dark time in the history of public health when political appointees overrule expert recommendations, pick and choose data to support their ideology, and use their position to advance personal agendas,” said Dr. Daniel Griffin, an infectious disease expert at Columbia University.

The F.D.A. has been profoundly changed since the Trump administration took charge. About 15 percent of its staff, or roughly 3,000 employees, have recently left or were fired. Some departures were so disabling for the agency that officials scrambled to hire employees back.

Dr. Makary, the F.D.A. commissioner, has given Dr. Prasad authority across the agency with the role of chief medical and scientific officer, in addition to appointing him to oversee the vaccine, cell and gene therapy division.

Some see the changes as a hopeful sign: Dr. Prasad rose to prominence as an academic who exhorted the F.D.A. to reserve its stamp of approval for drugs that demonstrated crystal-clear benefits. (He has said recently that he will be more flexible with drugs for rare diseases.)

Others view his sweeping authority with concern, given his shift during the pandemic toward frequent and sometimes expletive-laden critiques of policies and people who disagreed with his views on Covid safety measures.

Mr. Nixon of H.H.S. said the expanding roles for Dr. Prasad were a “response to years of fragmented decision-making that often lacked evidence-based judgment.”

Disagreement at the F.D.A. over Covid vaccines and other drug approvals is not unheard-of. In 2021, two top vaccine specialists left the agency over concerns about the decision to offer Covid boosters at an interval that they viewed as too close to the initial vaccine rollout.

Dr. Peter Marks, who preceded Dr. Prasad as the head of the vaccine and gene therapy division, overruled staff scientists who opposed approval of a drug to treat Duchenne muscular dystrophy, a rare condition that tends to be deadly for younger adults. Some patient groups applauded Dr. Marks’s decisions, which they believed recognized the need for a risky option when facing imminent decline and death.

Before joining the F.D.A., Dr. Prasad criticized Dr. Marks for the Duchenne drug decisions, saying on social media that he was an ally of pharmaceutical companies and “did kill that boy,” referring to a teenager who died from acute liver failure linked to the therapy.

After a second teenager’s death in recent weeks, also related to liver failure, a known side effect of the drug, Dr. Prasad announced a safety review.

Dr. Marks defended his actions, saying that he felt “terribly” about the deaths and that “there’s always benefit and risk in everything we do, and we take some risk, and hopefully we learn from it.”

He added: “I‘m the first to admit that my regulatory decision-making was not always perfect, but it was well intentioned and respectful of process, and respectful of patients, patient advocates, their families.”

Dr. Prasad stands to face similar scrutiny if his view of Covid as a waning threat turns out to be wrong. Dr. Peter Hotez, a vaccine expert at Baylor College of Medicine in Texas, said Dr. Prasad’s memos failed to account for the risk of long Covid and other complications linked to the virus, such as blood clots and heart problems. “I think that that’s a big mistake,” he said.

Dr. Griffin said that the memos did not acknowledge that myocarditis, an inflammation of the heart muscle, had been tied to the virus at a rate that is seven to 16 times that of cases linked to the vaccine, and had been a more serious complication from the virus.

“So if you want to lower the risk of myocarditis in this population with ongoing Covid cases,” Dr. Griffin said, “vaccination is safer than not vaccinating.”

About 30 staff scientists at the F.D.A. signed off on giving approval to the Novavax vaccine for anyone 12 or older on March 28, according to the newly released documents. Records show that they reviewed several studies, including a clinical trial of the vaccine involving 30,000 people, and a safety database with 45,000 adults and adolescents who got the vaccine.

In the large study, there were three cases of myocarditis within two weeks of the second dose, compared with one case in the placebo group.

The review also identified more cases of atrial fibrillation in the vaccinated group than in the placebo group, which the reviewers asked Novavax to study further.

The vaccine was 90 percent effective in preventing Covid illnesses among the study participants. F.D.A. staff scientists concluded that the main study “supports approval of the vaccine, and the risk-benefit assessment for this vaccine technology remains favorable,” the review said.

A Novavax spokeswoman did not comment directly on the memo, and Moderna declined to comment.

The new Moderna vaccine, called mNexspike, was developed with a dose that is one-fifth of the original formula. It was tested against the original Moderna vaccine in a study that included about 11,000 people and that found the new formula was slightly more effective.

The F.D.A. staff reviewers concluded that its safety profile was similar to the company’s original vaccine. About 30 agency staff members, many doctorate-level scientists or doctors, signed off on the decision, which concluded that no safety concerns were identified in the new Moderna version.

In the memos on both vaccines, Dr. Prasad said that the risk of severe illness from Covid had fallen sharply over the last four years. According to data from the Centers for Disease Control and Prevention, deaths and hospitalizations from Covid in 2024 and 2025 fell below the levels from the previous years. At least 32,000 deaths, mostly among older adults, were reported from October 2024 through June 7.

Dr. Prasad wrote that the former approach to updating the vaccines was akin to the strategy for the seasonal flu, but that it might not fit. He reasoned that Covid evolves more slowly than the flu, and that the protection from previous infections was more robust.

“It is important to acknowledge times at which the potential for benefit from vaccination among non-high-risk individuals is small and poorly defined,” Dr. Prasad wrote in the Novavax memo.

The F.D.A. and vaccine makers agreed to conduct studies of 50- to 64-year-old people who received the vaccine and a placebo to learn more about the shots in that age group.

The broader F.D.A. changes in Covid vaccine policy do not affect people 65 and older, but call for sharply limiting the shots only to younger people with a medical condition that put them at high risk.

Public health experts warned that the ramifications could be problematic for consumers. Insurers might balk at covering off-label prescriptions, which in turn could restrict access to the vaccine. Amid a patchwork of state laws, retail pharmacies could also face limits or liability.

Those concerns have also been raised about other changes made unilaterally by Robert F. Kennedy Jr., the head of the Health and Human Services Department. He recently dropped the recommendation that pregnant women receive the Covid vaccine. And he altered the recommendation for healthy children so that it now requires consultations with doctors or medical providers before vaccination. Those policy shifts are also expected to lessen use of the Covid shots.