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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 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 — 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.

“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.”