Robert Califf, a former Food and Drug Administration commissioner, is the Biden administration’s choice to once again head the agency, as it plays a critical role in efforts to fight the Covid-19 pandemic.

President Biden announced the nomination on Friday, sparking criticism among some lawmakers and patient advocates while a leading industry trade group leapt to his support. Dr. Califf is expected to be confirmed.

The...

Robert Califf, a former Food and Drug Administration commissioner, is the Biden administration’s choice to once again head the agency, as it plays a critical role in efforts to fight the Covid-19 pandemic.

President Biden announced the nomination on Friday, sparking criticism among some lawmakers and patient advocates while a leading industry trade group leapt to his support. Dr. Califf is expected to be confirmed.

The FDA, which has been clearing the use of Covid-19 vaccines, boosters and drugs, has been operating without a permanent leader since Mr. Biden took office.

“As the FDA considers many consequential decisions around vaccine approvals and more, it is mission critical that we have a steady, independent hand to guide the FDA,” Mr. Biden said.

Yet some lawmakers and advocacy groups were quick to express opposition to the nomination, citing Dr. Califf’s ties to the pharmaceutical industry at a time when a debate over lowering the cost of prescription drugs has taken center stage in Washington.

Sen. Joe Manchin (D., W.Va.), who voted against confirming Dr. Califf in 2016, said he would oppose his nomination once again, meaning Mr. Biden’s pick will require support from Republicans to clear the Senate.

“I urge the Administration to nominate an FDA Commissioner that understands the gravity of the prescription drug epidemic and the role of the FDA in fighting back against the greed of the pharmaceutical industry,” he said.

The White House, nonetheless, expressed confidence the nomination would prevail without any major obstacles, noting Dr. Califf was confirmed by an 89-4 vote when he last led the FDA.

The Pharmaceutical Research and Manufacturers of America, an industry trade group known as PhRMA, said it welcomed a nominee who understands the FDA’s role “in promoting public health and providing science-based oversight of our nation’s medicine supply.”

If confirmed, Dr. Califf, a prominent Duke University cardiologist who has worked with drugmakers on clinical trials and served at the helm of the FDA in 2016 and early 2017, will take over from Acting Commissioner Janet Woodcock. Dr. Califf ran the agency toward the end of the Obama administration.

He would lead an agency, which has a $6 billion budget and staff of 18,000 people, that has been working on tight timelines to determine whether experimental Covid-19 shots and medicines work safely for broad use.

The FDA has also been making decisions about e-cigarettes and prescription drugs for Alzheimer’s and other diseases.

Politico reported earlier that Mr. Biden was preparing to nominate Dr. Califf.

The long work hours and heavy demands generated by the pandemic have sapped morale among some inside the agency, which has also faced criticism of bowing to political pressure to authorize broad use of Covid-19 boosters.

The position has been open for about 10 months while the administration has filled many other top agency jobs.

Mr. Biden has struggled to find a nominee in part because there was a lack of interest in the job and because various interest groups have sparred over possible nominees, one person familiar with the deliberations said.

Consumer-advocacy groups such as Public Citizen have urged the administration not to nominate Dr. Califf, saying his past consulting experience with drugmakers would make him too friendly to the pharmaceutical industry.

Children aged 5 to 11 started getting their first doses of Covid-19 vaccines Wednesday after the CDC recommended use of the Pfizer-BioNTech shot for that age group. Some parents said they were eager for kids to get vaccinated and return to normal life. Photo: Maddie McGarvey/WSJ The Wall Street Journal Interactive Edition

When Dr. Woodcock’s name was floated, some consumer-advocacy groups and Democratic lawmakers pushed back, saying they questioned the role that a division she had headed played in the opioid crisis. Dozens of other health-related groups, however, supported her in a letter.

Consumer-advocacy groups lobbied for Dr. Joshua Sharfstein, who was principal deputy commissioner of the agency during the Obama administration. Some industry groups opposed his selection, another person familiar with the deliberations said.

The vacancy must be filled by Nov. 15 under the Federal Vacancies Reform Act, which establishes procedures for filling vacancies in an appointed office.

Mr. Biden’s pick for the job, Dr. Califf, has the support of several healthcare leaders but he could face opposition in the Senate.

Some lawmakers, including Sen. Bernie Sanders (I., Vt.), fought his nomination in 2016 during the Obama administration because they worried his ties to pharmaceutical companies would lead to him being too soft on industry.

At the Duke University School of Medicine, Dr. Califf is a cardiologist and researcher. He is considered a leading expert on clinical trials.

He has worked as a consultant for pharmaceutical companies such as AstraZeneca PLC, Merck & Co. and Johnson & Johnson. Since November 2019, he has advised Alphabet Inc.’s Google Health and Verily healthcare subsidiaries on strategy and policy.

If his nomination is approved, Dr. Califf will shepherd the FDA through the continuing pandemic and controversies such as its approval of Biogen Inc.’s Alzheimer’s drug Aduhelm over the objection of agency statisticians who said there was insufficient evidence to support approval.

Dr. Woodcock asked in July for a federal investigation of doctors within her own agency who met with the makers of the Alzheimer’s drug before the medicine’s approval.

Two career scientists who played leading roles regulating vaccines at the FDA recently left the agency, after helping write a piece, published in The Lancet medical journal, saying current evidence didn’t support broad use of Covid-19 boosters.

The National Institutes of Health will be losing its longtime director, Dr. Frances S. Collins, who is stepping down at the end of the year. The NIH often collaborates with the FDA.

Write to Stephanie Armour at stephanie.armour@wsj.com and Sabrina Siddiqui at Sabrina.Siddiqui@wsj.com