The Justice Department has issued subpoenas demanding confidential patient information from more than 20 doctors and hospitals that provide gender-related treatments to minors, according to officials with knowledge of the move.

The action marks a new turn in the Trump administration’s efforts to limit transgender medical care. Most of the subpoenas, issued through the consumer protection unit of the department’s civil division, attempt to pierce powerful federal confidentiality protections for patients and their medical providers.

Officials briefed on the investigation described the action as a fact-finding mission, an effort to determine whether any laws have been broken and a spur to kick-start negotiations with the providers over transgender treatment policy.

Investigators could eventually seek criminal charges if evidence of fraud is uncovered, officials said. But critics say the motivation is more political than investigative — a campaign of intimidation.

The subpoenas are part of a coordinated effort between the Justice Department and the White House to fulfill President Trump’s promises to curtail pediatric gender care. Pam Bondi, the attorney general, said in a statement Wednesday that “medical professionals and organizations that mutilated children in the service of a warped ideology will be held accountable.”

Revelations of the subpoenas come in the wake of a Supreme Court decision that upheld state laws banning youth gender medicine in about half the country. Hospitals and doctors in other states, where legislatures are unlikely to enact such bans, have faced increasing threats from the federal government. In response, a small number of clinics have limited their treatments or closed altogether.

It is unclear which hospitals and doctors received the subpoenas. But in May, nine leading children’s hospitals across the country received letters from the Centers for Medicare and Medicaid Services, demanding data on revenue from pediatric gender treatments and the rates of regret among patients, according to a person with knowledge of the effort.

Those letters applied explicit financial pressure to the hospitals. Dr. Mehmet Oz, the head of the agency, wrote that it “has an obligation to be a good steward of taxpayer dollars.” He added, “Hospitals accepting federal funds are expected to meet rigorous quality standards and uphold the highest level of stewardship when it comes to public resources.”

Other agencies have also been applying increased pressure to meet Mr. Trump’s demands.

In June, the F.B.I. put out a call to the public to report hospitals and doctors who were performing surgeries on minors.

And on Wednesday, the Federal Trade Commission hosted a daylong event devoted to the question of whether providers of transgender medical treatments were engaging in unfair or deceptive trade practices. A top Justice Department official, appearing at the event, announced that manufacturers of drugs used in such care were under investigation for possible violations of drug marketing laws, in addition to the subpoenas to health care providers.

Gender treatments for minors, which can include puberty-blocking drugs, hormones and, in rarer cases, surgeries, are at the center of fierce medical debate around the world.

Many clinicians and families in the United States and elsewhere have said that the treatments can be profoundly beneficial for transgender adolescents. While the number of minors who medically transition is small, demand for the treatments has increased in recent years, and countries have taken different approaches. Health agencies in England, Sweden and Finland have limited the treatments, citing the uncertain evidence of the benefits and the possible risks, which can include loss of fertility. Meanwhile, Germany has cautiously endorsed the treatments, citing the lack of effective alternatives.

None of these governments have banned the care or prosecuted hospitals or providers.

In the United States, a coalition of critics of youth gender medicine from both the right and the left have argued for banning the treatments. But now that most Republican-led states have already enacted such laws, the strategy appears to have shifted to singling out specific hospitals and providers in states without restrictions in place.

Multiple clinicians working at gender clinics in blue states declined to comment on the subpoenas and other recent actions, citing fears that doing so would endanger them and their patients.

“This politically motivated effort is a drastic overreach and a backhanded attempt to intimidate providers and institutions serving the transgender youth population,” said Dr. Scott Leibowitz, a child and adolescent psychiatrist who led a youth gender clinic in Columbus, Ohio, until that state’s ban took effect last year. The Justice Department’s subpoenas, he added, will create “widespread fear for every patient in the country who will be wondering when or if their private health care records will be released.”

Opponents of gender-related treatments called out specific doctors and hospitals during the discussions hosted by the F.T.C. on Wednesday, sometimes drawing from medical records and internal hospital presentations to argue that they had misled patients and insurers.

Also prominently featured were several young adults who transitioned as adolescents and later regretted it. While studies are limited, researchers estimate that 5 to 10 percent of patients choose to detransition.

“We need to make sure that no more kids are sold a product they can’t return,” said one panelist, Claire Abernathy, who underwent testosterone treatment and a mastectomy at age 14 and later detransitioned.

But the F.T.C. does not have authority over the practice of medicine, said Samuel Levine, the former head of the agency’s Bureau of Consumer Protection.

“The F.T.C. is in the business of commercial regulation, not medical decision-making,” said Mr. Levine, who led cases against companies falsely advertising supplements, stem cell treatments and addiction treatments during his tenure. “This is a significant departure from F.T.C. norms and a clear politicization of consumer protection.”

At least two hospitals, in Los Angeles and Pittsburgh, have decided to shut down their youth gender clinics entirely, citing mounting pressure from the Trump administration.

Children’s Hospital Los Angeles notified staff members in June that the clinic would shutter in late July. In an email, it told employees that the potential termination of federal funds — which account for 65 percent of its annual funding and enable it to be the largest pediatric safety net provider in California — would be “an existential threat to our hospital operations."

The Los Angeles and Pittsburgh children’s hospitals are among the nine that received the demand letter from Dr. Oz this spring; the others are in Boston, Philadelphia, Denver, Oakland, Cincinnati, Seattle and Washington. All of them appear on the so-called Dirty Dozen list of major providers identified by the activist group Do No Harm, which helped craft state bills banning pediatric gender medicine.

The group’s chairman, Dr. Stanley Goldfarb, a kidney specialist who was a former dean at the University of Pennsylvania’s medical school, said in an interview that his organization had worked with the Trump administration and that threats of funding cuts were key to the effort.

The federal government’s “ability to restrict payment is going to be a big influence,” he said.

At Wednesday’s F.T.C. event, speakers were asked to suggest next steps, now that the Supreme Court has allowed state bans of gender medicine for minors.

On the panel was Dr. Ethan Haim, a Texas surgeon who was indicted last year for releasing private medical information about transgender youth treatments; federal prosecutors under the Trump administration dropped the charges against Dr. Haim, who called himself a whistle-blower. On Wednesday, he argued that doctors providing this care should be prosecuted to create a chilling effect across the country.

“Then these people will be held accountable,” he said, “And there’s a very good chance this will stop even in blue states.”

Jordan Campbell, a fellow panelist who represented several detransitioners in malpractice lawsuits and now works for the Justice Department, responded, “Working on it, Dr. Haim.”

David McCabe and Reed Abelson contributed reporting.