Dr. Califf was confirmed for the job in a vote of 89 to 4; in addition to Mr. Manchin, Senators Edward J. Markey, Democrat of Massachusetts; Richard Blumenthal, Democrat of Connecticut; and Kelly Ayotte, Republican of New Hampshire, voted against him. But other Republicans, led by Senator Mitch McConnell of Kentucky, then the majority leader, voted in favor.

That support may be one reason Mr. Biden picked Mr. Califf: His selection drew mixed reaction.

“It is surprising that the White House has seemed really tone-deaf on conflicts of interest and very close ties to the industry,” said Diana Zuckerman, the president of the National Center for Health Research, a nonprofit advocacy group.

But others said they believed that Dr. Califf’s industry experience should not bar him from the job, noting that he has disclosed his ties in publishing the results of clinical trials.

“The truth of the matter is industry develops drugs — you have to work with industry. The issue is disclosure in publication,” said Ellen V. Sigal, the founder and chairwoman of the nonprofit Friends of Cancer Research, which accepts industry funding. “Rob has done many, many clinical trials with industry, but he has not been a pawn of industry. He’s completely committed to transparency, integrity and science.”

Dr. Aaron S. Kesselheim, who served on the F.D.A. advisory panel that considered the Alzheimer’s drug and resigned from the committee after it was approved, said Dr. Califf’s background running clinical trials would be valuable for leading the agency.

“I don’t think it’s necessarily disqualifying,” said Dr. Kesselheim, a professor of medicine at Harvard Medical School and Brigham and Women’s Hospital. “I think the fact that he worked for such a long time in clinical trials demonstrates that he has expertise in understanding what goes into a good clinical trial. Hopefully, he can bring that into his role as an F.D.A. commissioner.”

But Dr. Kesselheim objected to Dr. Califf’s efforts, when he was the commissioner, to allow drug companies to advertise off-label uses for their products, noting that patients can be endangered by drugs that are prescribed for uses that the F.D.A. has not approved. “That to me is a red flag,” Dr. Kesselheim said. “Hopefully, he’s moved past that as an idea, because it would be a terrible idea.”