But despite the White House refusal to approve the new vaccine guidance document, the F.D.A. published the guidelines in briefing materials to an advisory committee that will discuss them on Thursday, effectively making them official. And nearly two weeks after Mr. Trump called the antibody treatment he received when sick with Covid-19 a miraculous “cure” and said that he had authorized it, the F.D.A. has not yet approved it.

Internally, Dr. Hahn has tried to erect a shield between his staff and White House officials, asking that all calls be routed directly to him and not to his staff. His situation is especially fraught because Mr. Trump has openly accused the F.D.A. of engaging in political ploys to harm his re-election chances. Alex M. Azar II, the secretary of health and human services and Dr. Hahn’s direct superior, has also questioned Dr. Hahn’s motives in some conversations with the White House, according to multiple officials…

In what might be the final months of the Trump administration, and close enough to the election to make his firing unlikely, Dr. Hahn seems to be trying to save the F.D.A. from the fate of its sister agency, the Centers for Disease Control and Prevention, whose scientists have been stripped of much of their authority and independence in responding to the pandemic.

“It’s better late than never, but I do think we can see a lot of damage has been done,” said Dr. Jesse L. Goodman, the F.D.A.’s chief scientist from 2009 to 2014. “And I don’t think they are out of the woods yet.”