Robert F. Kennedy Jr., President-elect Donald J. Trump’s choice to lead the nation’s health agencies, formally asked the Food and Drug Administration to revoke the authorization of all Covid vaccines during a deadly phase of the pandemic when thousands of Americans were still dying every week.

Mr. Kennedy filed a petition with the F.D.A. in May 2021 demanding that officials rescind authorization for the shots and refrain from approving any Covid vaccine in the future.

Just six months earlier, Mr. Trump had declared the Covid vaccines a miracle. At the time Mr. Kennedy filed the petition, half of American adults were receiving their shots. Schools were reopening and churches were filling.

Estimates had begun to show that the rapid rollout of Covid vaccines had already saved about 140,000 lives in the United States.

The petition was filed on behalf of the nonprofit that Mr. Kennedy founded and led, Children’s Health Defense. It claimed that the risks of the vaccines outweighed the benefits and that the vaccines weren’t necessary because good treatments were available, including ivermectin and hydroxychloroquine, which had already been deemed ineffective against the virus.

The petition received little notice when it was filed. Mr. Kennedy was then on the fringes of the public health establishment, and the agency denied it within months. Public health experts told about the filing said it was shocking.

John Moore, a professor of immunology at Weill Cornell Medical College, called Mr. Kennedy’s request to the F.D.A. “an appalling error of judgment.” Gregg Gonsalves, an epidemiologist at the Yale School of Public Health, likened having Mr. Kennedy lead the federal health agencies to “putting a flat earther in charge of NASA.”

Dr. Robert Califf, commissioner of the Food and Drug Administration, described Mr. Kennedy’s effort to halt the use of Covid vaccines as a “massive error.”

Mr. Kennedy’s transition spokeswoman did not respond to requests for comment, but has said recently that he does not want to take vaccines away.

Asked in November by an NBC reporter about his general opposition to Covid vaccines — and whether he would have stopped authorization — Mr. Kennedy said he was concerned that the vaccines did not prevent transmission of the virus.

“I wouldn’t have directly blocked it,” he said. “I would have made sure that we had the best science, and there was no effort to do that at that time.”

Mr. Kennedy’s early opposition to Covid vaccines has alarmed public health experts, many of whom contend that it should disqualify him from overseeing health agencies with the power to authorize, monitor and allocate funding for millions of vaccines each year.

They are also concerned about how he might handle a possible bird flu pandemic, which could necessitate a rapid deployment of vaccines.

As Mr. Kennedy prepares for his confirmation hearings before two Senate committees, he and his allies have insisted that he is not anti-vaccine.

In fact, in mid-2023, he told a House panel that he had taken all recommended vaccines — except for the Covid immunization.

At his confirmation hearings, he’ll most likely face scrutiny of his broader statements on vaccines, including that the polio vaccine cost more lives than it saved.

Mr. Trump has stepped forward in recent weeks to defend Mr. Kennedy after The New York Times reported that one of Mr. Kennedy’s lawyers had previously petitioned the F.D.A. to revoke approval or pause distribution of several polio vaccines over safety concerns.

“I think he’s going to be much less radical than you would think,” Mr. Trump said last month.

After the Times report, Mr. Trump and Mr. Kennedy expressed their support for the polio vaccine.

If confirmed by the Senate as secretary of the Health and Human Services Department, Mr. Kennedy would assume oversight of $8 billion in funding for the Vaccines for Children program and would have the authority to appoint new members to a panel that makes influential vaccine recommendations to states.

At the time Mr. Kennedy challenged the Covid vaccines, some of his objections touched on wider concerns about their rapid development. Emergency-use authorization — a preliminary form of approval — for immunizations was unusual. Others argued that a public health emergency dictated a speedier rollout.

Dr. Jennifer Nuzzo, director of the Pandemic Center at Brown University School of Public Health, said it would be reasonable to debate whether Covid vaccines should have been subject to additional study.

But she profoundly disagreed with Mr. Kennedy’s views, saying that “the idea that in early 2021 that you could be saying that people over the age of 65 don’t need Covid vaccines — that’s just nuts.”

Vaccines have rare side effects, and there have been cases of injury from the Covid shots. Government officials weigh the harms against the potential to save lives. An estimate released in early 2024 found that the Covid vaccines and mitigation measures saved about 800,000 lives in the United States.

Another study found that in late 2021 and 2022, Covid death rates among unvaccinated people were 14 times the rates of those who had received a Covid booster shot. Researchers also estimated that from May 2021 through September 2022, more than 230,000 deaths could have been prevented among people who declined initial Covid inoculations.

From the start of the Covid vaccine campaign, Mr. Kennedy’s view that the Covid vaccines were dangerous put him at odds with Mr. Trump, whose Operation Warp Speed to develop the vaccines was one of his policy triumphs. And Mr. Kennedy went on a concerted campaign against the vaccine.

Mr. Kennedy told Louisiana lawmakers in late 2021 that the Covid vaccine was the “deadliest vaccine ever made.”

He has remained a plaintiff in a lawsuit against President Biden and others, contesting efforts by government officials to limit his ability to suggest on social media that Covid vaccines were not safe.

In January 2021, Mr. Kennedy suggested on Facebook that the death of the baseball legend Hank Aaron, 86, was related to a Covid vaccine he had received 17 days earlier. It was “part of a wave of suspicious deaths” following Covid vaccines, he claimed. A doctor who was vaccinated alongside Mr. Aaron and the county medical examiner dismissed the claim.

In May, when Mr. Kennedy petitioned the F.D.A. to “immediately remove Covid vaccines from the market,” he was joined by Dr. Meryl Nass, a member of the Children’s Health Defense scientific advisory board and a physician in Maine.

Her medical license was initially suspended on an emergency basis in early 2022 for prescribing ivermectin and hydroxychloroquine to patients with severe cases of Covid, including one who was intubated, Maine medical board records show.

She later sued the board, claiming that it retaliated against her for exercising her right to free speech. The case is pending.

In 2022, Mr. Kennedy and others filed a lawsuit against the F.D.A. on behalf of Children’s Health Defense and parents who said they were concerned that their children would be given Covid vaccines without their knowledge or consent. The amended lawsuit, filed in July 2022, sought a court order requesting that the agency reconsider granting authorization for Pfizer and Moderna Covid vaccines for children.

A Texas appeals court dismissed the case in early 2024, concurring with a lower court that the plaintiffs did not face a “concrete or imminent” risk of harm. In June, the Supreme Court declined to hear an appeal.

Mr. Kennedy also sent letters to the F.D.A. threatening legal action if vaccine authorizations for children were granted.

Covid vaccines by Pfizer and Moderna for infants and children 6 months to 11 years old remain in use under emergency authorization, according to the F.D.A. Spokesmen for Pfizer and for Moderna said the companies are pursuing full approval for all ages.

Mr. Kennedy claimed in the censorship case that top Biden administration officials had coerced social media platforms to silence him, mostly during the summer of 2021. At the time, vaccine rates were stalling. People who were not vaccinated began to die at higher rates. Some who died were young; their loved ones said they were confused by conflicting messages on social media — or regretted that they had not gotten the vaccine.

Records in the lawsuit outline a briefing that summer with Jen Psaki, the White House press secretary at the time, and Dr. Vivek Murthy, the U.S. surgeon general, both of whom criticized social media companies for allowing the spread of misinformation that was influencing people against vaccination.

“And we can’t wait longer for them to take aggressive action because it’s costing people their lives,” Dr. Murthy said on July 15, 2021.

Mr. Biden expressed outrage the following day, telling reporters that social media companies that hosted vaccine misinformation were “killing people.”

In legal filings, Mr. Kennedy said that he had been named one of the “Disinformation Dozen” by a prominent advocacy group — and that he was one of the people the White House was targeting. Exhibits in the lawsuit show that White House officials leaned on social media companies to take down misinformation.

Within a month, a senior Facebook executive reported to Dr. Murthy that it had removed a number of pages or groups, including Mr. Kennedy’s, court records show.

The Supreme Court dismissed an associated case last summer, and an appeals court dismissed Mr. Kennedy’s case late last year. Lawyers representing Mr. Kennedy and others are still working on obtaining depositions of about 30 people, mostly Biden administration officials.

Sheryl Gay Stolberg and Dylan Freedman contributed reporting.