Dr. Robert Califf, who was F.D.A. commissioner during the Obama administration and has supported Dr. Sharpless, said the learning curve at the agency is steep. “It takes six months to figure out where the bathrooms are,” he said. “The loss of continuity seems like a big negative.”

Some health interest groups said they were looking forward to working with Dr. Hahn. In a statement, the American Heart Association urged Dr. Hahn to address rising rates of teen nicotine addiction, and to carry out a promised ban on flavored e-cigarettes that has not yet come to fruition.

“We welcome the nomination of a permanent F.D.A. commissioner at a time when the agency’s role to protect and promote public health is only growing in importance,” the association’s chief executive, Nancy Brown, said in a statement.

Another group reacted with dismay to the news that Dr. Giroir would be assuming the commissioner’s duties until Dr. Hahn is confirmed, saying that Giroir had overseen cuts to the office that administers federal funding for family planning and reproductive health.

“We do not want to see the F.D.A. entangled in the politics around reproductive health and women’s health,” Cynthia A. Pearson, executive director of the National Women’s Health Network, said in a statement.

Dr. Hahn specializes in lung cancer and sarcoma. He has moved up the ranks at M.D. Anderson since arriving in 2015, when he served as chairman of the radiation oncology department. In 2017, he was named the hospital’s chief operating officer and in 2018, the chief medical executive. Before coming to M.D. Anderson, he was chairman of the radiation oncology department at the University of Pennsylvania’s Perelman School of Medicine from 2005 to 2014.

Dr. Hahn has donated to Republicans in the past, though not to the Trump campaign. In 2017, he gave $1,000 to the New Pioneers PAC, a group affiliated with Representative Greg Walden, Republican of Oregon, who was then chairman of the House Energy and Commerce Committee, which oversees the F.D.A. In earlier election cycles, he donated to candidates from both parties, including $706 to Mitt Romney, the Republican presidential nominee, in 2012 and $250 to the congressional campaign of Rep. John Murtha, a Democrat, in 2008.