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The weaknesses in the command structure have played out in disparate ways. In the case of the booster rollout, the White House appeared to overstep its bounds and left itself open to accusations that political considerations were coloring decision-making. More frequently, Dr. Walensky has announced changes in public health guidance without anyone fully vetting them with colleagues, leading to backtracking and revisions.

The team of “docs,” as Mr. Biden likes to call them, includes Dr. Walensky; Dr. Woodcock; Dr. Fauci, the director of the infectious disease division at the National Institutes of Health; and Dr. David Kessler, the chief science officer at the Department of Health and Human Services, whose duties include stocking the pandemic toolbox with vaccines and treatments. Mr. Biden’s health secretary, Xavier Becerra, a former California attorney general, is their boss, but several current and former White House officials said he plays a limited role in setting pandemic policy — a characterization that Mr. Becerra disputes.

Dr. Walensky’s announcement in May that fully vaccinated people need not wear a mask or physically distance from others, indoors or outdoors, was an example of uncoordinated policymaking.

Mr. Biden and Mr. Zients had indicated publicly that such a change might be coming. But some White House aides learned of the change only the night before Dr. Walensky announced it to the public, and there was no coordinated strategy in place to explain or defend it.

“It wasn’t like, ‘OK, let’s have a Zoom call tonight about the pros and the cons of the mask mandate.’ That didn’t happen,” Dr. Fauci said. Asked whether he tried to modify Dr. Walensky’s decision beforehand, he said, “You have to know the decision is being made before you modify it.”

The C.D.C.’s announcement last month that it was shortening the recommended isolation period for people with Covid was another bout of confused messaging. At first, the agency announced that people with resolving symptoms could stop isolating after five days without recommending they get a negative test first. But after that omission drew criticism from outside experts, the agency tweaked its guidance to say that if people have access to tests and want to use them, “the best approach is to use an antigen test towards the end of the five-day isolation period.”