Just minutes into the first meeting of new scientific advisers appointed by Health Secretary Robert F. Kennedy Jr., it was clear that the skeptical panelists intended to upend longstanding vaccine recommendations in the United States, particularly those pertaining to children.

The meeting on Wednesday marked a remarkable and fraught moment in public health. Mr. Kennedy has replaced the gatekeepers of immunization policy in the United States, mostly scientists with deep expertise, with people who often have been critical of vaccine safety and efficacy.

The panel, called the Advisory Committee on Immunization Practices, advises the Centers for Disease Control and Prevention on vaccine policy. Its determinations have a powerful impact.

Insurance companies and government programs like Medicaid are required to cover immunizations that the C.D.C. recommends, and states base their school mandates on the agency’s guidance.

Martin Kulldorff, formerly a professor of medicine at Harvard University and the committee’s chair, began the meeting by inviting people to share their criticism of vaccines and chastising the media for fanning the “flames of vaccine hesitancy” by labeling some new panelists as anti-vaccine.

Dr. Robert Malone, a chair of the panel, has said he considers the label “anti-vaxxer” to be “high praise.” At the meeting, Dr. Kulldorff noted that he had been fired from Harvard for refusing to get a Covid-19 shot because he “already had immunity” from infections.

Dr. Kulldorff added that the panel would evaluate the effect of all the shots given to children and adolescents, including a vaccine for hepatitis B given at birth that is credited with nearly eliminating maternal transmission of that disease.

“In addition to studying and evaluating individual vaccines, it’s important to evaluate the cumulative effect of a recommended vaccine schedule,” he said.

Dr. Richard Besser, who served as the acting director of the C.D.C., said: “It’s deeply concerning to me that — within minutes of the meeting starting — the new A.C.I.P. chair immediately sought to cast doubt on the safety and effectiveness of childhood vaccines.”

“I’m worried that this is a harbinger of even worse things to come,” he added.

Other experts said Dr. Kulldorff’s mention of the hepatitis B vaccine, also a frequent target of Mr. Kennedy, was an unwelcome sign.

“This and other remarks suggests that they are indeed going to be moving in a direction that will restrict access to safe, effective childhood vaccines,” said Dr. Fiona Havers, who resigned last week from her position as a senior C.D.C. adviser on vaccine policy.

Dr. Havers quit after Mr. Kennedy fired all 17 members of A.C.I.P. He named eight new members, at least half of whom have expressed deep skepticism of some vaccines.

The meeting was marked by drama even before it began.

The panelists were announced barely two weeks ago; usually they are vetted for months, even years. Three of them have taken part in lawsuits casting doubt on the safety or efficacy of vaccines, public records show.

Senator Bill Cassidy, Republican of Louisiana and chairman of the Senate health committee, whose vote cinched Mr. Kennedy’s confirmation as health secretary, called for the meeting to be delayed, saying the new panelists lacked experience and ideological diversity.

One of the eight new members named by Mr. Kennedy, Dr. Michael Ross, withdrew from the committee on Tuesday.

Breaking with decades of tradition, the American Academy of Pediatrics boycotted the meeting, saying “we won’t lend our name or our expertise to a system that is being politicized at the expense of children’s health.”

A roll call of liaisons from other organizations, such as the American College of Obstetrics and Gynecology, did not occur until after the lunch break, raising fears that they would not be allowed to speak.

When one liaison member inquired about their inability to unmute their microphones, a C.D.C. official responded in an email viewed by The New York Times: “Sorry. I’m not in control.” Mr. Kennedy and the agency’s director’s office have “taken over,” the official added.

On Wednesday, many empty chairs lined the tables where normally as many as 19 scientists are seated. Two of the seven new panelists — Dr. Cody Meissner, a pediatric infectious disease physician at Tufts University, and Vicky Pebsworth, a nurse affiliated with an anti-vaccine group — attended remotely.

C.D.C. staff members who oversee the panel and organize data workshops preceding the meeting were replaced or reassigned before the meeting. The agency also does not have a director to sign off on the recommendations, which is the usual procedure.

On Thursday, Lyn Redwood, a former leader of Children’s Health Defense, the anti-vaccine group founded by Mr. Kennedy, is scheduled to present recommendations on a version of the flu vaccine that contains thimerosal.

Ms. Redwood has been hired as a special government employee at the Department of Health and Human Services, according to an agency official who spoke on condition of anonymity for fear of retaliation.

Thimerosal is a mercury-based preservative in vaccines that has been shown in dozens of studies to be harmless. It has not been a component of most childhood vaccines since 2001, yet Mr. Kennedy and other critics have insisted that the preservative may be linked to rising rates of autism.

A scientific review of evidence showing the safety of thimerosal posted by C.D.C. scientists on Tuesday was taken down. “This document by the C.D.C. vaccine safety office did not go through the appropriate process to be posted,” an H.H.S. spokesman told The Times.

Ms. Redwood’s presentation initially included a slide with references to studies that did not exist, Reuters reported on Tuesday. By Wednesday, that slide had been removed from her presentation.

But her presentation still maintained that the flu vaccine contains 50 micrograms of thimerosal, double the actual amount in the shot, noted Dr. David Boulware, an infectious diseases professor at the University of Minnesota.

“If the ‘thimerosal expert’ cannot truthfully convey how much thimerosal is present in influenza vaccines, that is a basic factual lapse,” Dr. Boulware said.

The panel had been expected to vote on Wednesday on clesrovimab, a new monoclonal antibody approved by the Food and Drug Administration earlier this month, as an alternative to protect infants from the respiratory syncytial virus.

Another monoclonal antibody, nirsevimab, sharply reduced R.S.V. hospitalizations among infants during the 2024-25 season, and so far does not appear to pose safety concerns apart from some cases of hives, according to data presented at the meeting.

But less than an hour before the scheduled vote, Dr. Kulldorff said the committee would ask questions about the data and vote on Thursday instead.

The committee also skipped discussions on expanding R.S.V. vaccines for adults 50 and older who are at high risk, which the previous committee members had endorsed.

A dozen or more C.D.C. scientists typically present data to A.C.I.P. panelists. This time, only a few senior scientists were in attendance. Dr. Adam MacNeil, a senior epidemiologist, offered detailed data on Covid-19.

Dr. Kulldorff asked about the results of double-blind randomized clinical trials on the Covid vaccines, evidently hoping to point out that such trials have not been conducted since the vaccines were first authorized.

Dr. Meissner questioned the Covid hospitalization data. He made a distinction between hospitalizations for or with Covid, an issue frequently brought up during the pandemic by scientists who questioned whether harms of the virus were exaggerated.

Outside experts took issue. “The hospitalization ‘with’ versus ‘for’ Covid is a standard Covid minimizer trope,” said Dr. Sean O’Leary, the chair of the infectious disease committee at the American Academy of Pediatrics.

Dr. Meissner’s implication that serious harm from Covid is rare in children is “misinformation,” he said. “Rates in children under six months are similar to adults 65 to 74 years, which is not rare.”

Dr. Malone and other committee members asked probing questions about the safety of the Covid vaccines, questioning whether the C.D.C. had adequately investigated side effects from the shots.

The agency has looked “forwards and backwards and sideways” at the possible side effects, and has not found any associations beyond those it has already detailed, Dr. Sarah Meyer, the C.D.C. scientist who presented the data, said in response.

The panel will not vote on Covid shot recommendations at this meeting, because a preliminary meeting scheduled for June 12 was not convened.

On Thursday, the panelists will also revisit federal recommendations for how young children should receive a vaccine for measles, mumps, rubella and chickenpox that has been available since 2005.

Four in five Americans, including a majority of Republicans and supporters of the Make America Great Again movement, say that children should be vaccinated against preventable diseases to attend school, according to a poll released on Wednesday by the Harvard T.H. Chan School of Public Health and the de Beaumont Foundation.