For decades, as an activist, Robert F. Kennedy Jr. resisted the scientific consensus that vaccines are safe and necessary to prevent serious disease. Now at the helm of the nation’s health department, he has begun to put his extreme views into practice, ousting veteran scientists and installing allies across the nation’s health agencies to enact major shifts in vaccine policy.

Some of Mr. Kennedy’s hires are activists who have worked for years alongside him. Others are scientists who say they broadly support vaccines but publicly criticized Covid shots or mandates during the pandemic. Many of these scientists have begun to question the safety or value of other shots, reflecting the views of Mr. Kennedy. The following account is based on previous statements made by these officials and on interviews with current and former health agency leaders.

The agency’s new vaccine lead and chief medical officer, Dr. Vinay Prasad, has called himself an “extreme pro-vaccine person,” and Dr. Marty Makary, the agency’s commissioner, said last week that “we believe in vaccines.”

But the two officials, who sharply criticized vaccine mandates as academic researchers during the pandemic, have expressed doubts about the safety and necessity of Covid boosters for healthy children and adults. This summer, Dr. Prasad overrode some agency scientists who favored widespread access to Covid shots, narrowing the vaccine’s eligibility to those 65 and older and to younger people with underlying medical conditions.

Last week, Dr. Makary echoed the views of Mr. Kennedy when he publicly questioned the longstanding recommendation to give the hepatitis B vaccine at birth. That shot is credited with nearly eliminating the transmission of the disease from mother to infant.

Dr. Prasad replaced a veteran at the agency, Dr. Peter Marks, who resigned in March and said that Mr. Kennedy’s aggressive stance on vaccines posed a danger to the public.

In June, Mr. Kennedy fired all 17 members of a powerful C.D.C. expert panel, the Advisory Committee on Immunization Practices. Insurance companies and government programs like Medicaid are required to cover the vaccinations that the panel recommends.

Mr. Kennedy handpicked eight new members that month, half of whom had expressed skepticism of vaccines at some point. (One has since stepped down.) Others have little expertise in immunology or vaccines.

On Monday, Mr. Kennedy appointed five more members, just days before the group meets to review recommendations for multiple vaccines. Some of the newly selected members have been critical of Covid vaccines or vaccine mandates.

Dr. Robert Malone is a controversial figure. He performed early experiments using mRNA in the 1980s but gained notoriety during the pandemic for claiming that Covid vaccines were unsafe, contradicting volumes of studies.

Martin Kulldorff, a biostatistician, has been generally supportive of vaccines but opposed Covid vaccination for children and vaccine mandates. Vicky Pebsworth, a nurse with a doctorate in public health, serves on the board of the National Vaccine Information Center, a nonprofit that disseminates misinformation about the risks of vaccination.

Dr. Malone and Dr. Kulldorff have served as paid expert witnesses in legal cases against vaccine makers. Dr. Pebsworth claimed in a lawsuit that a survey of families of unvaccinated children supported a hypothesis that a rise in the number of recommended childhood vaccines explained an epidemic of chronic disease.

Another panel member, Retsef Levi, is a management and health analytics expert at the Massachusetts Institute of Technology. He has been critical of a variety of vaccines and has called for Covid vaccines to be pulled from the market.

Dr. Evelyn Griffin, an obstetrician and gynecologist, questioned the safety and effectiveness of Covid vaccines in a hearing in the Louisiana House of Representatives in 2021. Dr. Kirk Milhoan, a pediatric cardiologist, questioned the safety and effectiveness of Covid vaccines at a 2024 event led by Representative Marjorie Taylor Greene, Republican of Georgia. Catherine M. Stein is an epidemiology professor who in 2022 called for an end to Covid vaccine mandates at universities.

Dr. Cody Meissner is a professor of pediatrics who opposed vaccine mandates and has questioned the ongoing need for Covid vaccines for children and pregnant women. He previously served on the advisory committee and is widely considered to be the most qualified member.

The others are not known to have spoken out against vaccines. They are Dr. Joseph R. Hibbeln, a nutritional neuroscientist; Dr. James Pagano, an emergency medicine physician; Hillary Blackburn, a pharmacist; and Dr. Raymond Pollak, a surgeon and transplant specialist.

The C.D.C. director has the power to accept or reject the immunization committee’s recommendations. The current acting director is Mr. Kennedy’s deputy at the Department of Health and Human Services, Jim O’Neill, a former biotechnology executive. The previous director, Susan Monarez, said she was forced out because she would not agree to accept the newly re-formed committee’s recommendations.

A special adviser to the C.D.C. director, Stuart Burns, is a critical player driving the health secretary’s agenda at the agency. Mr. Burns has been quietly working to remake the immunization committee and its agenda.

Mr. Burns is not a scientist but he worked for decades as a staff member for Republican congressmen known for their vaccine skepticism. One is Dr. Dave Weldon, a former representative from Florida who was also Mr. Kennedy’s original choice for C.D.C. director. The White House withdrew Dr. Weldon’s nomination just hours before his confirmation hearing because some Senate Republicans were concerned about his stance on vaccines.

Mr. Burns works closely with three other Kennedy hires who serve H.H.S. but also work closely with the C.D.C. Dr. Reyn Archer is a former Texas health commissioner who has questioned the safety and value of the Covid vaccine on social media. He serves as a liaison between the health secretary’s office and the C.D.C., and has been helping Mr. Burns to develop and guide the immunization committee.

David Geier is a steadfast figure in the anti-vaccine movement who has spent more than 20 years trying to establish a link between vaccines and autism, despite scientific consensus that there is none. Mr. Geier, who is listed as a senior data analyst in the H.H.S. directory, was given access to federal data on post-vaccination side effects and is using it to continue his studies on autism.

Lyn Redwood is a nurse practitioner and the former head of Children’s Health Defense, the anti-vaccine group founded by Mr. Kennedy. Since the early 2000s, Ms. Redwood has criticized the use of mercury as a preservative in vaccines. She has said she believes the ingredient is linked to her son’s autism.

Now listed as an expert at H.H.S., Ms. Redwood gave a presentation in June to the immunization committee, a role usually reserved for C.D.C. scientists. She said that the mercury preservative in vaccines, known as thimerosal, was toxic to children, even though dozens of studies have shown it is harmless in this form. The panel later voted to stop recommending the already limited number of flu vaccines that contained the preservative.

Dr. Matthew Memoli is a veteran infectious disease scientist at the National Institutes of Health who now serves as its principal deputy director. As a senior researcher under Dr. Anthony Fauci during the pandemic, Dr. Memoli opposed Covid vaccine mandates and declined to get a shot himself.

Since becoming a leader of the research agency, Dr. Memoli has downplayed the value of vaccines for certain respiratory diseases, according to the whistle-blower complaints of two prominent scientists.

Dr. Jay Bhattacharya, the N.I.H director, sharply criticized vaccine mandates as an academic researcher during the pandemic. He co-wrote an anti-lockdown treatise in 2020 with Dr. Kulldorff, one of Mr. Kennedy’s selections for the C.D.C. immunization committee.

During his confirmation hearing in March, Dr. Bhattacharya reiterated his support for childhood vaccinations for diseases like measles. He also said he was “convinced” vaccines did not cause autism, even as he urged more research on the question, which scientists say has long been settled.