Dr. Robert M. Califf, an academic and clinical trial researcher who ran the agency in 2016, has also consulted for pharmaceutical companies.WASHINGTON — President Biden announced on Friday that he would nominate Dr. Robert M. Califf, a former commissioner of the Food and Drug Administration, to lead the agency again. His decision ends nearly a year of political wrangling as the White House vetted then dropped several candidates after complaints that some were too close to the pharmaceutical industry.In the end, White House officials might have concluded that they could not find a suitable candidate with no industry ties. Dr. Califf, 70, a respected academic and clinical trial researcher who ran the agency during the last year of the Obama administration, has long been a consultant to drug companies and ran a research center at Duke University that received some funding from the drug industry.The agency is sorely in need of permanent leadership. Since Margaret Hamburg, who served as commissioner for most of the Obama administration, left in 2015, the F.D.A. has had seven different commissioners — some acting, some permanent — including Dr. Califf, who served for just 11 months after Dr. Hamburg’s departure. And recently, its reputation for independence has come under attack.The F.D.A. has been front and center in the federal government’s response to the coronavirus pandemic. It has the authority to approve Covid vaccines, tests and treatments, as well as certain types of protective equipment. It was also widely criticized for allowing manufacturers to flood the market with inaccurate Covid tests early in the pandemic and for failing to stand up to Mr. Biden’s predecessor, Donald J. Trump, who at times promoted unproven and unsafe treatments.“Dr. Califf is one of the most experienced clinical trialists in the country, and has the experience and expertise to lead the Food and Drug Administration during a critical time in our nation’s fight to put an end to the coronavirus pandemic,” Mr. Biden said in a statement. “As the F.D.A. considers many consequential decisions around vaccine approvals and more, it is mission critical that we have a steady, independent hand to guide the F.D.A. I am confident Dr. Califf will ensure that the F.D.A. continues its science and data drive decision-making.”During his previous stint as commissioner, Dr. Califf sought to permit pharmaceutical companies to advertise off-label uses for F.D.A.-approved products, a practice that is not permitted under the strict regulations governing drug advertising. But the proposal, which many public health experts considered dangerous, was blocked by others in the Obama administration, according to a person familiar with it.A cardiologist who has seen the harmful effects of smoking on the heart, Dr. Califf has been a forceful advocate for tobacco control; before he was the F.D.A. commissioner, he was the agency’s deputy commissioner for medical products and tobacco. In an appearance with other former commissioners this year, he said, “I have never seen more capable or nastier lawyers than what I experienced in trying to deal with the tobacco industry.”He added, “It was awesome and quite frightening for public health.”For the past two years, after stepping down as the vice chancellor for clinical and translational health at Duke University, Dr. Califf has worked as a senior adviser to Verily Life Sciences, a health technology firm, and its sister company Google Health. He has encouraged Verily to focus on addiction, cardiovascular health and management of chronic diseases, according to a person at the company who spoke on the condition of anonymity.Dr. Califf, who remains an adjunct professor of medicine at both Duke and Stanford University, is on the corporate board of Cytokinetics, a biopharmaceutical company, according to its website. He has received personal fees for consulting from Merck, Amgen, Biogen, Genentech, Eli Lilly and Boehringer Ingelheim, according to his Duke University biography.In a statement, Dr. Califf said he was honored to be nominated for the position “at a critical time for our country,” adding, “There’s a lot of work to do, and if confirmed I look forward to rejoining the great team at the F.D.A. to help in their inspiring mission to serve the public.”If Dr. Califf is confirmed by the Senate, he will again take the reins of an agency that is responsible for more than $2.8 trillion worth of food, medical products and tobacco. The Food and Drug Administration regulates products accounting for about 20 cents of every dollar spent by consumers in the United States.During the Trump administration, the agency granted an emergency use authorization for hydroxychloroquine that it later withdrew, and revised its emergency authorization of convalescent plasma to restrict its use.More recently, the agency’s dealings with Biogen, the maker of a newly approved drug for Alzheimer’s disease, have come under scrutiny. The Food and Drug Administration approved the drug, Aduhelm, which costs $56,000 annually, over the objections of its own independent advisers, who said there was insufficient evidence that it was effective.The acting commissioner, Dr. Janet Woodcock, subsequently called for a federal investigation, acknowledging that some of the agency’s interactions with Biogen “may have occurred outside of the formal correspondence process.”Dr. Janet Woodcock is the acting commissioner of the Food and Drug Administration.Stefani Reynolds for The New York TimesDr. Woodcock, the agency’s longtime drug division chief, was once considered a front-runner for commissioner. But critics — notably Senator Joe Manchin III, Democrat of West Virginia — accused her of being too close to the pharmaceutical industry. He wrote to Mr. Biden this year, suggesting that Dr. Woodcock was responsible for the approval of opioid drugs that devastated his state and making clear that he would not vote to confirm her.Mr. Manchin also has close ties to industry. His daughter, Heather Bresch,was until last year the chief executive officer of Mylan Inc., a pharmaceutical company that owned the severe allergy treatment EpiPen, which was at the center of public outrage over high drug prices.Dr. Califf’s relationships with pharmaceutical companies as a clinical trials researcher proved to be a liability during his Senate confirmation process in 2016. Mr. Manchin blasted him for “big pharma ties” and voted against him.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.”During his first tenure at the agency, Dr. Califf focused on modernizing the collection and use of electronic health data to answer questions about drugs and medical devices that could not be gleaned from clinical trials.He also sought to increase the use of “real-world evidence” — case studies and individual patient experiences — to inform regulatory decisions. Some public health experts fear that relying on data outside of randomized clinical trials endangers patients; Dr. Califf believes there is room for both approaches.His willingness to consider such data caused controversy in 2016, when the Food and Drug Administration overruled its experts to approve a new drug for treatment of a rare, fatal muscle disease, despite lack of evidence that it worked.The drug, eteplirsen, was given conditional approval amid fierce lobbying by young muscular dystrophy patients, their parents and the drugmaker, Sarepta Therapeutics. Dr. Ellis F. Unger, who worked under Dr. Woodcock at the time, called the drug “essentially a scientifically elegant placebo.”But Dr. Woodcock won Dr. Califf’s support to overrule her staff and the advisory panel. The decision is considered within the agency as having laid the groundwork for the approval of Biogen’s drug for Alzheimer’s disease.