“If you have a commissioner who is that conflicted, recusal is a tricky business,” said Susan F. Wood, who resigned as the director of the F.D.A.’s Office of Women’s Health in 2005 in protest over the agency’s decision to delay over-the-counter approval of the morning-after pill.
Dr. Gottlieb’s nomination comes at a momentous time for the agency, which Mr. Trump has promised to significantly remake. The next commissioner will be charged with putting into practice a far-reaching law, passed in December, aimed at bringing drugs to market more quickly. Congress also must reauthorize a set of bills this year that determine how much the drug and medical device industry will pay in user fees, which fund more than half of the agency’s budget to review new drugs.
The president’s other appointments for high-profile health roles, such as Dr. Tom Price, the health and human services secretary, and Seema Verma, the administrator of the Centers for Medicare and Medicaid Services, have also come under fire for being too close to the businesses they regulate or for their investments in health care companies. Dr. Gottlieb’s newly disclosed financial forms are likely to draw similar criticism at his Senate confirmation hearing on April 5.
One line of inquiry could include a thorny issue that arose on Wednesday: The generic drugmaker Mylan announced that the F.D.A. had rejected its application to make a generic copy of the inhaler Advair Diskus, a best-selling product for GlaxoSmithKline. Dr. Gottlieb has called for making it easier to market generic versions of complex drugs like Advair to reduce prices, but he also received close to $90,000 in fees in 2016 and the first two months of this year as a Glaxo consultant, according to financial disclosures.
Some say a yearlong recusal would not suffice.
“The question is going to be, are you going to have to recuse yourself from all the decisions that are going to have an impact on that company?” said Dr. Wood, who is now an associate professor at George Washington University.
Leslie B. Kiernan, a lawyer for Dr. Gottlieb, said that his recusal plan was approved by federal ethics officials and that F.D.A. commissioners do not typically get involved in matters involving individual companies. “Every individual who goes into government from the private sector with experience in the industry is going to have some recusals,” she said. “The key role of the commissioner is to set broad policies for the agency.”
Others who know Dr. Gottlieb, including Democrats, praise his intellect and independent thinking, even as they acknowledge that he is likely to bring a more industry-friendly worldview to a sprawling agency of more than 16,000 employees. Dr. Gottlieb, 44, served as an F.D.A. deputy in the George W. Bush administration before leaving to do private consulting. With his medical training and government experience, he was considered the conventional choice over more radical candidates that Mr. Trump was said to be weighing.
“I think he is not so easily put into a box,” said Dr. Joshua M. Sharfstein, who was the agency’s deputy commissioner in the Obama administration. Dr. Sharfstein said he had sought Dr. Gottlieb’s advice when he took his job at the F.D.A., and the two have stayed in touch. “I think he has the capability to really grow into the role.”
In writings and speeches, Dr. Gottlieb has criticized the F.D.A., calling for more flexibility to permit access to drugs that provide strong clues — but not conclusive evidence — that they work. He has proposed ways to shake up the agency’s bureaucratic structure, suggesting that drug approvals be made by more seasoned senior staff members, and that a special team oversee drugs intended for rare diseases. In a departure from the agency position that it has little control over drug costs, Dr. Gottlieb has also shown a willingness to take on high prices by making it easier for certain generic drugs to be approved.
Some said Dr. Gottlieb’s background is what qualifies him for the job.
“The alternative is to have a leader who may have no conflicts because they’ve never been involved in the drug development process,” said Tim Coetzee, the chief advocacy, services and research officer at the National Multiple Sclerosis Society, which receives some funding from the drug industry and invests in drug development research. “We don’t think that is a sound approach.”
Dr. Gottlieb had little government experience beyond stints at the F.D.A. and the Centers for Medicare and Medicaid Services when he became an F.D.A. deputy at age 33 in 2005. He had been a financial analyst and consultant to the pharmaceutical industry, and wrote the Gilder Biotech Report and the Forbes Gottlieb Medical Technology Report.
Those industry associations soon became a headache. In late 2005, he was forced to recuse himself from proposals on the avian flu, The Boston Globe reported, because he had consulted for major vaccine players, including Roche and Sanofi. Around the same time, emails leaked to Time magazine showed him questioning career F.D.A. employees over a decision to stop a multiple sclerosis drug trial, and expressing surprise at the rejection of an osteoporosis drug.
Back then, Dr. Gottlieb defended his actions, saying he had to understand the agency’s process.
“The agency was being highly politicized by the Bush administration, and he certainly was part and parcel of that politicization,” Dr. Wood said. “I think for that subset of F.D.A. career staff, the physicians who worked there, I think there was suspicion of everyone in leadership at the time.”
While he was at the F.D.A., Dr. Gottlieb practiced medicine at a Connecticut hospital in his spare time, said John Taylor, a former F.D.A. lawyer who had worked with him. “Scott would work two shifts at a hospital and see patients on the weekends,” he said. “I thought he was Superman.”
In 2006, while he was a deputy commissioner, Dr. Gottlieb received a diagnosis of early-stage Hodgkins lymphoma, but he is now cancer free.
In 2007, Dr. Gottlieb returned to the private sector, becoming a partner at New Enterprise Associates, where he advised the firm’s health care team, and began consulting for a range of companies. Dr. Gottlieb also held seats on a number of corporate boards, including Tolero Pharmaceuticals, a Utah company working on cancer treatments, and MedAvante, which assists pharmaceutical companies with clinical trials.
According to the federal ethics filings, Dr. Gottlieb said he would resign from all outside boards. The yearlong recusal, he said, would remove him from decisions on all the companies he received payments from, including six that he held a financial interest in while at New Enterprise Associates, all health care providers or lab testing companies that are overseen by the Centers for Medicare and Medicaid Services. He also listed several biotech start-ups that he invested in through T.R. Winston & Co., a merchant bank.
Financial disclosure documents show Dr. Gottlieb made more than $3 million during 2016 and through March 1 of this year, including $1.85 million from T.R. Winston and $280,000 for consulting for New Enterprise, according to the disclosures, which were reported earlier by The Wall Street Journal. But the investments in T.R. Winston were not all in health care companies and included energy companies, as well as other firms.
Dr. Gottlieb, a resident scholar at the American Enterprise Institute, has also been a prolific writer and public speaker, criticizing the agency’s approach. “In so heavily prioritizing one of its obligations — the protection of consumers — the F.D.A. has sometimes subordinated and neglected its other key obligation, which is to guide new medical innovations to market,” Dr. Gottlieb wrote in 2012 in National Affairs, a conservative-leaning political journal.
Some of Dr. Gottlieb’s views have alarmed researchers who argue that rigorous study of drugs and medical devices is the best way to ensure they work. In 2014, Dr. Gottlieb criticized a medical device study that used “sham,” or dummy, procedures as a kind of placebo. The sham procedure, he argued, was invasive and unnecessary, especially since the product, called renal denervation, was already approved in Europe to lower patients’ blood pressure.
But at the time Dr. Gottlieb wrote the article, Medtronic, the device’s manufacturer, had already announced that the study had failed, and an article a month later in The New England Journal of Medicine showed that patients who underwent renal denervation did no better than those who received a fake procedure.
“Had we not done a sham control, the erroneous belief that this procedure worked would have persisted,” said Dr. Deepak L. Bhatt, one of the study’s principal investigators. He said Dr. Gottlieb’s argument that the trial was unethical baffled him. “I would think after seeing the results, any scientist or physician who understands clinical trials would come to the same conclusion, not the opposite conclusion.”
These days, the F.D.A. has shown a willingness to approve products that have shown promise based on intermediate measures, like a shrinking tumor, rather than long-term outcomes like survival rates — especially in cancer research. One recent study showed that the agency decides on drugs faster than its counterparts in Europe and Canada.
In December, President Obama signed into law the 21st Century Cures Act, which further directs the F.D.A. to remove barriers to approval, requiring that the agency consider the “least burdensome” means of showing the safety of medical devices, and consider feedback from patients.
One of the biggest jobs of the F.D.A.’s next leader, said Dr. Jerry Avorn, a professor at Harvard Medical School who studies the drug industry, will be translating that law into reality. “Whoever is the new commissioner,” he said, “is going is have both marching orders, and a blank slate.”
An earlier version of this article referred imprecisely to millions of dollars in recent earnings by Dr. Gottlieb. The income he received included payments from his involvement with T.R. Winston, a merchant bank. It has investments in a wide range of companies, some of which, but not all, are health care and drug companies. An earlier headline repeated the error.
An article on Thursday about Dr. Scott Gottlieb, nominated to be commissioner of the Food and Drug Administration, misidentified, in some copies, the university where Susan F. Wood is an associate professor. Dr. Wood, formerly with the F.D.A., now teaches at George Washington University, not at Georgetown.