His investments through New Enterprise Associates, a venture capital firm, and T.R. Winston & Company, an investment bank, were also called into question. Earlier in Dr. Gottlieb’s career, before attending the Mount Sinai School of Medicine, he worked as a health care investment banking analyst for Alex. Brown & Sons.

That experience, Dr. Gottlieb has said, benefits the F.D.A. because it helps him understand the industry. He has recused himself for two years from matters concerning about 20 companies with which he was associated — in accordance with the White House ethics pledge. The day he was sworn in, he sold all of his health-related stock, including investments in Tolero Pharmaceuticals, Collective Health and U.S. Renal Care, according to a financial report filed with the Office of Government Ethics. He purchased government bond funds.

Like most of Mr. Trump’s appointees, Dr. Gottlieb has also hired industry lawyers and lobbyists whose former clients often have business before the agency. Among them are Jack Kalavritinos, an associate commissioner who had lobbied for the device maker Covidien, now owned by Medtronic, for seven years; Nina Devlin, a senior communications adviser who was the head of global communications at Mylan, makers of the EpiPen; and Rebecca K. Wood, who was a partner in the law firm Sidley Austin and is now the agency’s top lawyer.

According to her financial disclosure forms, Ms. Wood did legal work for many of the drug industry’s largest companies and trade groups, including AbbVie, Bayer, St. Jude Medical and the Medical Information Working Group, which favors the expansion of off-label uses for drugs. She also worked for New Enterprise Associates, in which Dr. Gottlieb was a venture partner. An agency spokeswoman said that Ms. Wood has had to recuse herself already from several matters, but declined to detail the issues involved.

A balancing act

By taking a more conventional approach to the job, Dr. Gottlieb stands out among other presidential appointees, some of whom have aggressively rolled back regulations or are curtailing the scope of their agencies’ powers, as at the Environmental Protection Agency and the Department of Energy.

He has already disagreed with an administration position, objecting to a plan to move an international food-safety division to the trade office, saying it would hurt the country’s reputation as a food watchdog.

The administration backed down on the trade matter, but Dr. Gottlieb has been forced to compromise on other issues. Last October, he questioned proposals backed by Vice President Mike Pence and others that would give terminally ill patients greater access to experimental treatments. He did make a concession — promising that the F.D.A. would find a way to make it easier for patients to get some of those treatments, although he noted that the agency already approves 99 percent of such requests. Mr. Trump also recently told Republican lawmakers that Dr. Gottlieb was leading the effort to get legislation passed by Congress.