Two leaders of the office had publicly questioned whether the general population needed coronavirus booster shots and recently announced plans to retire.,

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A top F.D.A. official moved on Monday to take over the agency’s vaccines office.

Dr. Peter Marks, one of the Food and Drug Administration’s highest-ranking regulators, on Capitol Hill earlier this year.Credit…Anna Moneymaker for The New York Times

Sept. 27, 2021Updated 4:45 p.m. ET

Dr. Peter Marks, one of the Food and Drug Administration’s highest-ranking regulators, on Monday took over the agency’s vaccines office, whose two leaders had publicly questioned whether the general population needed coronavirus booster shots.

Dr. Marks said in an email to staff that the move, which makes him acting director of the office, would allow the two — Dr. Marion Gruber, the director of the vaccines office, and Dr. Philip Krause, her deputy — to “take care of close-out activities prior to departing and help to assure a smooth transition.”

Dr. Gruber recently announced plans to retire at the end of October, and Dr. Krause in November.

Both have evaluated vaccines for decades at the agency’s Office of Vaccines Research and Review, and were said to have been upset at the Biden administration’s announcement last month that booster shots would be available to most adults by the week of Sept. 20, contingent on F.D.A. clearance.

The two regulators wrote in The Lancet earlier this month that there was no credible evidence yet in support of booster shots for the general population, and that more data and public discussion were needed. Their position was shared by many independent scientists, who have said that coronavirus vaccines continue to be powerfully protective against severe illness and hospitalization.

After a tense meeting of the F.D.A.’s vaccine advisory panel, Dr. Gruber last week signed the agency’s decision memo behind its authorization of Pfizer-BioNTech booster shots for people 65 and older, people at high risk of severe Covid-19 and others at risk of serious complications from Covid-19 whose jobs frequently expose them to the virus.

The C.D.C.’s vaccine advisory panel delivered a similar vote, but not did endorse offering boosters based on one’s job. Dr. Rochelle P. Walensky, the agency’s director, overruled the advisers and recommended shots for people based on “occupational or institutional setting.”

President Biden said last week that 60 million people would be eligible for a Pfizer-BioNTech booster over the coming months.

The F.D.A.’s vaccines office has more important decisions ahead, including whether to authorize the Pfizer-BioNTech vaccine for children ages 5 to 11 and booster shots for recipients of the Moderna and Johnson & Johnson vaccines.

As director of the F.D.A.’s Center for Biologics Evaluation and Research, Dr. Marks, a hematologist and oncologist, has supervised the vaccine office’s reviews for the entirety of the pandemic. He is credited as the architect of the Trump administration’s vaccine program, Operation Warp Speed, that developed and funded coronavirus vaccines.

But Jesse Goodman, a former chief scientist at the agency, said that Dr. Marks’s decision to take over the office was “extremely unusual and concerning.” He said that the F.D.A. needed to offer a clear explanation, or else it could “erode trust” in the agency. “This just doesn’t make sense to me,” he said.

Understand Vaccine and Mask Mandates in the U.S.

Vaccine rules. On Aug. 23, the Food and Drug Administration granted full approval to Pfizer-BioNTech’s coronavirus vaccine for people 16 and up, paving the way for an increase in mandates in both the public and private sectors. Private companies have been increasingly mandating vaccines for employees. Such mandates are legally allowed and have been upheld in court challenges.Mask rules. The Centers for Disease Control and Prevention in July recommended that all Americans, regardless of vaccination status, wear masks in indoor public places within areas experiencing outbreaks, a reversal of the guidance it offered in May. See where the C.D.C. guidance would apply, and where states have instituted their own mask policies. The battle over masks has become contentious in some states, with some local leaders defying state bans.College and universities. More than 400 colleges and universities are requiring students to be vaccinated against Covid-19. Almost all are in states that voted for President Biden.Schools. Both California and New York City have introduced vaccine mandates for education staff. A survey released in August found that many American parents of school-age children are opposed to mandated vaccines for students, but were more supportive of mask mandates for students, teachers and staff members who do not have their shots. Hospitals and medical centers. Many hospitals and major health systems are requiring employees to get a Covid-19 vaccine, citing rising caseloads fueled by the Delta variant and stubbornly low vaccination rates in their communities, even within their work force.New York City. Proof of vaccination is required of workers and customers for indoor dining, gyms, performances and other indoor situations, although enforcement does not begin until Sept. 13. Teachers and other education workers in the city’s vast school system will need to have at least one vaccine dose by Sept. 27, without the option of weekly testing. City hospital workers must also get a vaccine or be subjected to weekly testing. Similar rules are in place for New York State employees.At the federal level. The Pentagon announced that it would seek to make coronavirus vaccinations mandatory for the country’s 1.3 million active-duty troops “no later” than the middle of September. President Biden announced that all civilian federal employees would have to be vaccinated against the coronavirus or submit to regular testing, social distancing, mask requirements and restrictions on most travel.

“These are the two people who know the most about vaccines at the F.D.A., and they should be doing everything they can to keep them involved in all the critical activities,” he said, referring to Dr. Gruber and Dr. Krause.

Some administration officials said Dr. Marks’s action made sense because the upcoming departures of Dr. Gruber and Dr. Krause could delay critical decisions on vaccines if someone else were not in charge. Dr. Eric Topol, a professor of molecular medicine at Scripps Research in La Jolla, Calif., praised Dr. Marks’s experience, and said that “new leadership was vital” after Dr. Gruber and Dr. Krause so strongly expressed that booster shots were not justified for everyone.

But Dr. Luciana Borio, a former acting chief scientist at the F.D.A. under President Barack Obama, said Dr. Marks could have tapped someone else. “There are several well-qualified individuals in the office,” she said, “and I was surprised that one of them wasn’t being elevated to acting director.”

An F.D.A. spokeswoman said in a statement Monday that “a smooth transition is particularly important given the critical regulatory submissions that the Office of Vaccines Research and Review will need to work through as a team over the coming months that will affect the health of nearly every American.”