Marty Makary resigned from his position as commissioner of the US Food and Drug Administration (FDA) on Tuesday, concluding a 13-month tenure at the regulatory agency that frequently drew the ire of the White House, Congress, industry and the public, Donald Trump confirmed on Tuesday.

Kyle Diamantas, who previously worked as the top food official at the agency setting the strategic direction and operations for food policy in the US, has been reported as Makary’s acting replacement, according to Politico, which first reported the resignation and Makary’s replacement.

Trump signed off on a plan to fire Makary earlier this month, after the president scolded the FDA chief for not approving fruit-flavored vapes, according to the Wall Street Journal.

“He seems fine,” Trump responded when asked about Makary on Friday. When pressed if he would fire Makary, Trump said: “I’ve been reading about it, but I know nothing about it.”

On Tuesday, Trump told reporters at the White House that Makary is “a great guy” but “was having some difficulty”.

“He’s a great doctor and he was having some difficulty, but he’s going to go on and he’s going to do well. Everybody wants that job,” Trump added.

Makary initially overrode agency scientists to halt the approval of the first fruit vapes on the market before the FDA announced the approval would move forward last week.

The vapes weren’t the first stand Makary had taken as the FDA chief. He also clashed with lawmakers on Capitol Hill about drug regulation decisions and a review of mifepristone, an abortion medication, that conservative members of Congress accused him of slow-walking. There is abundant scientific evidence on the safety and importance of mifepristone.

The FDA also reportedly stopped the publication of research on the safety of vaccines against shingles and Covid, demonstrating a “pattern” of “not letting information out that might support the general safety of vaccines”, said Janet Woodcock, former acting FDA commissioner. Other controversial decisions on vaccines included a refusal to consider Moderna’s new flu vaccine, a decision that was soon reversed after public backlash.

The Trump administration has shied away from discussing its unpopular changes to routine vaccine recommendations before the midterm elections.

“Vaccines have really gotten their attention,” said Peter Lurie, executive director of the Center for Science in the Public Interest and a former associate commissioner at the FDA. “They do understand that they’ve gone too far for the American people on vaccines.”

The FDA’s “mismanagement and bungled drug reviews” have “chilled investments in life-saving, innovative cures”, Darin LaHood, a Republican congressman from Illinois, said at the House ways and means committee budget hearing last month. Ron Johnson, a Republican senator from Wisconsin, said in March that he was investigating the FDA for rejections of rare disease treatments.

Waves of layoffs and the appointment of inexperienced officials have created a “massive upheaval that has been an ongoing feature of daily work at FDA ever since the new administration began”, Lurie said. “It’s just endless chaos.”

There have also been concerns about revamped guidelines for clinical trials, the commissioner’s new priority review vouchers and “data-free” regulatory decisions.

Several key positions in the Trump administration still remain vacant. Neither Nicole Saphier, Trump’s third pick for US surgeon general, nor Erica Schwartz, who would be the fifth director of the US Centers for Disease Control and Prevention (CDC) in the past year, have yet undergone the confirmation process before the Senate. Jay Bhattacharya, the director of the National Institutes of Health, is temporarily leading the CDC.