During his Senate confirmation hearings to be health secretary, Robert F. Kennedy Jr. presented himself as a supporter of vaccines. But in office, he and the agencies he leads have taken far-reaching, sometimes subtle steps to undermine confidence in vaccine efficacy and safety.

The National Institutes of Health halted funding for researchers who study vaccine hesitancy and hoped to find ways to overcome it. It also canceled programs intended to discover new vaccines to prevent future pandemics.

The Centers for Disease Control and Prevention shelved an advertising campaign for the flu shot. Mr. Kennedy has said inaccurately that the scientists who advise the C.D.C. on vaccines have “severe, severe conflicts of interest” in promoting the products and cannot be trusted.

The Health and Human Services Department cut billions of dollars to state health agencies, including funds needed to modernize state programs for childhood immunization. Mr. Kennedy said in a televised interview on Wednesday that he was unaware of this widely reported development.

The Food and Drug Administration canceled an open meeting on flu vaccines with scientific advisers, later holding it behind closed doors. A top official paused the agency’s review of Novavax’s Covid vaccine. In a televised interview last week, Mr. Kennedy said falsely that similarly created vaccines don’t work against respiratory viruses.

Some scientists said they saw a pattern: an effort to erode support for routine vaccination, and for the scientists who have long held it up as a public health goal.

“This is a simultaneous process of increasing the likelihood that you will hear his voice and decreasing the likelihood that you’ll hear other voices,” Kathleen Hall Jamieson, director of the Annenberg Public Policy Center, said of Mr. Kennedy.

He is “decertifying other voices of authority,” she said.

H.H.S. disagreed that Mr. Kennedy was working against vaccines.

“Secretary Kennedy is not anti-vaccine; he is pro-safety,” Andrew Nixon, a department spokesman, said in a statement. “His focus has always been on ensuring that vaccines are rigorously tested for efficacy and safety.”

The statement continued, “We are taking action so that Americans get the transparency they deserve and can make informed decisions about their health.”

After attending the funeral of an unvaccinated child who died of measles in West Texas on Sunday, Mr. Kennedy endorsed the measles vaccine on X as “the most effective way to prevent the spread of measles.”

But he has also described vaccination as a personal choice with poorly understood risks and suggested that miracle treatments were readily available. On Sunday, he praised two local doctors on social media who have promoted dubious, potentially harmful, treatments for measles.

Even as cases of measles in the United States have surged past 600 in 22 jurisdictions, Mr. Kennedy has claimed in a recent interview that the measles vaccine causes deaths every year (untrue); that it causes encephalitis, blindness and “all the illnesses that measles itself causes” (untrue); and that the vaccine’s effect wanes so dramatically that older adults are “essentially unvaccinated” (untrue).

According to an email obtained by The New York Times, H.H.S. intends to revise its web pages to include statements like “The decision to vaccinate is a personal one” and “People should also be informed about the potential adverse events associated with vaccines.” (Vaccines are already administered only after patients provide informed consent, as required by law.)

Tensions with mainstream experts came into sharp focus last week, when Dr. Peter Marks, the top vaccine regulator, resigned under pressure from the F.D.A.

“It has become clear that truth and transparency are not desired by the secretary, but rather he wishes subservient confirmation of his misinformation and lies,” Dr. Marks said in his resignation letter.

Mr. Kennedy’s position on vaccines has raised alarm for decades. But it has become particularly notable now, against a backdrop of rising skepticism of vaccines and worsening outbreaks of measles and bird flu, experts said.

The M.M.R. vaccine — a combination product to prevent measles, mumps and rubella that has been available since 1971 — has long been a target of anti-vaccine campaigns because of the disproved theory that it can cause autism. Mr. Kennedy has said that he would like to revisit the issue, in part to assuage parents’ fears that the vaccines are unsafe.

But he has hired David Geier to re-examine the data. Senator Bill Cassidy, Republican of Louisiana, a doctor and the chairman of the Senate Health Committee, has sharply criticized the decision to spend tax dollars testing a discredited hypothesis even as the administration is cutting billions for other research.

“If we’re pissing away money over here,” he said last month, “that’s less money that we have to actually go after the true reason.”

The refusal to accept scientific consensus is “disturbing, because then we get into very strange territory where it’s somebody’s hunch that this does or doesn’t happen, or does or doesn’t work,” said Stephen Jameson, president of the American Association of Immunologists.

In interviews, Mr. Kennedy has downplayed risks of measles and emphasized what he sees as the benefits of infection.

“Everybody got measles, and measles gave you protected lifetime protection against measles infection — the vaccine doesn’t do that,” he said in an interview on Fox News.

Two doses of the M.M.R. vaccine do provide decades-long immunity. And while immunity from the infection may last a lifetime, “people also suffer the consequences of that natural infection,” Dr. Jameson said.

One consequence was discovered just a few years ago: A measles infection can destroy the immune system’s memory of other invading pathogens, leaving the body vulnerable to them again.

Measles kills roughly 1 in every 1,000 infected people, and 11 percent of those infected this year have been hospitalized, many of them children under 5, according to the C.D.C. Two girls, ages 6 and 8, died in West Texas.

By contrast, side effects after vaccination are uncommon. But Mr. Kennedy has suggested that people should apprise themselves of the risks before opting for the shot.

The phrasing implies that “if you are more fully informed, you might make a different decision,” said Dr. Jamieson, of the Annenberg center.

Doctors have long expected health secretaries and the C.D.C. to urge widespread vaccination unequivocally amid an outbreak, and in the past they have.

But Mr. Kennedy has spoken enthusiastically about cod liver oil, a steroid and an antibiotic that are not standard therapies. Some of those treatments may be making children more sick.

“The messaging I’m seeing is focused on potential treatments for measles,” said Dr. Sean O’Leary, chair of the infectious disease committee for the American Academy of Pediatrics.

Closed Doors

At his confirmation hearing, Mr. Kennedy promised that he would not change the C.D.C.’s childhood vaccination schedule. About two weeks later, he announced a new commission that would scrutinize it.

The schedule is based on recommendations from the Advisory Committee on Immunization Practices, a panel of medical experts who review safety and effectiveness data, potential interactions with other drugs and the ideal timing to maximize protection.

At his confirmation hearing, Mr. Kennedy claimed that 97 percent of A.C.I.P. members had financial conflicts of interest. He has long held, without evidence, that federal regulators are compromised and are hiding information about the risks of vaccines.

“It’s frankly false,” said Dr. O’Leary, who serves as a liaison to the committee from the pediatric academy.

Mr. Kennedy’s statistic came from a 2009 report that found that 97 percent of disclosure forms had errors, such as missing dates or information in the wrong section.

In fact, A.C.I.P. members are carefully screened for major conflicts of interest, and they cannot hold stocks or serve on advisory boards or speaker bureaus affiliated with vaccine manufacturers.

On the rare occasion that members have indirect conflicts of interest — for example, if an institution at which they work receives money from a drug manufacturer — they disclose the conflict and recuse themselves from related votes.

The committee’s votes were public and often heavily debated.

“When I was C.D.C. director, people flew in from Korea and all over the world to observe the A.C.I.P. meetings, because they were a model of transparency,” said Dr. Thomas R. Frieden, who led the agency from 2009 to 2017.

Mr. Kennedy has repeatedly promised greater transparency and accountability, but he has proposed ending public comment on health policies.

His department canceled a meeting of the A.C.I.P. in February at which members were set to discuss vaccines for meningitis and flu, rescheduling it for April.

The department also canceled a meeting to discuss the seasonal flu vaccine. Officials met later without the agency’s scientific advisers.

“After all that conversation about how they want to be transparent, one of the first things he does is take things behind closed doors and diminish the amount of public input we’re getting,” said Dr. Georges Benjamin, executive director of the American Public Health Association.

At his confirmation hearing, Mr. Kennedy repeated a fringe theory that Black Americans should not receive the same vaccines as others because they “have a much stronger reaction.”

Senator Angela Alsobrooks, Democrat of Maryland, who is Black, admonished him for his “dangerous” opinion: “Your voice would be a voice that parents would listen to.”

Two weeks later, at a clinic for teenage mothers in Denver, a 19-year-old woman refused all vaccines for herself and her 1-year-old son — including the measles and chickenpox shots he was supposed to have that day.

She told the pediatrician, Dr. Hana Smith, who described the incident, that she had read online that vaccines were bad for people with more melanin in their skin.

There are reams of evidence to the contrary. Still, it quickly became clear to Dr. Smith that nothing was going to change her patient’s mind.

“No matter how much information I can give to the contrary on it, the damage is already done,” Dr. Smith said.

Misinformation is particularly difficult to counter, Dr. Smith said, “when it’s someone that has a leadership position, especially within the health care system.”