Donald Trump has nominated vaccine sceptic and former Democrat Robert F Kennedy Jr as head of the US Department of Health and Human Services, the latest in a series of controversial picks for top cabinet jobs.

The appointment will put Kennedy, who sowed doubts about Covid-19 vaccines and has been critical of the pharmaceutical industry, in charge of a department with a $1.8tn budget with wide-ranging influence over drug regulation and public health.

The move hit the stock market, as investors digested the prospect of tougher political outlook in the world’s biggest pharmaceutical market. US-listed vaccine makers including Moderna and BioNTech both closed down over 5 per cent on Thursday. On Friday European pharma groups fell, with GSK and Sanofi losing more than 3 per cent.

Trump said in a statement on Thursday that he was “thrilled” to nominate Kennedy to the role. “For too long, Americans have been crushed by the industrial food complex and drug companies who have engaged in deception, misinformation, and disinformation when it comes to Public Health,” the president-elect said.

Trump has roiled Washington in recent days with a series of controversial cabinet nominations, raising questions about how many will make it through the Senate approval process. On Wednesday, he tapped loyalists Matt Gaetz as attorney-general and Tulsi Gabbard to be director of national intelligence.

Trump said that as head of HHS, with oversight of agencies such as the Food and Drug Administration and the Centers for Disease Control and Protection, Kennedy would “restore these Agencies to the traditions of Gold Standard Scientific Research, and beacons of Transparency, to end the Chronic Disease epidemic, and to Make America Great and Healthy Again!”

During the final weeks of his presidential election campaign Trump had said he would “let [Kennedy] go wild on health, go wild on the food . . . go wild on medicines”. Drugmakers had expressed concern about the possibility of Kennedy being given a formal role in the administration.

Thanking Trump for his nomination, Kennedy wrote on X: “I look forward to working with the more than 80,000 employees at HHS to free the agencies from the smothering cloud of corporate capture so they can pursue their mission to make Americans once again the healthiest people on Earth.”

The Consumer Brands Association, whose members include Nestlé and PepsiCo, noted that the agencies within HHS “operate under a science and risk-based mandate and it is critical that framework remains under the new administration”.

Kennedy, the son of the late attorney-general Robert Kennedy, beat a number of other candidates for the job, including former housing secretary and neurosurgeon Ben Carson and ex-Louisiana governor Bobby Jindal, according to a person close to discussions.

The nomination repays Kennedy for dropping his own campaign for the presidency and backing Trump instead, helping to deliver votes for the former president, the person said.

Kennedy’s nomination as the country’s top health official is likely to spark alarm among public health experts and pharmaceutical groups. He has described the Covid-19 jab as “the deadliest vaccine ever made” and last year said the virus was “ethnically targeted” to spare Ashkenazi Jews and Chinese people.

Democrat Senator Ron Wyden, chair of the Senate finance committee, said after the announcement that Kennedy’s “outlandish views on basic scientific facts are disturbing and should worry all parents who expect schools and other public spaces to be safe for their children”.

Bill Cassidy, the top Republican on the Senate health committee, praised the pick, and said Kennedy “championed issues like healthy foods and the need for greater transparency in our public health infrastructure”.

Kennedy has said he would reorient government resources to tackle chronic disease instead of spending money on prescription drugs, as well as floating the idea of removing fluoride from the water system and to take on food companies over the additives in food.

In an interview with NBC News last week, Kennedy insisted that “if vaccines are working for somebody, I’m not going to take them away. People ought to have choice.” But he added that he would remove “entire departments” of the FDA.

Kennedy’s appointment sets the stage for some of his allies to be appointed to other health agencies, such as the FDA, CDC and the National Institutes of Health. Healthcare influencers and entrepreneur siblings Calley and Casey Means, who are advising Kennedy, as well as Stanford professor Jay Bhattacharya, who opposed the widescale rollout of Covid-19 vaccines, have been jockeying for positions, according to a person close to discussions.

Health officials from Trump’s former administration, including Joe Grogan, Eric Hargan and Paul Mango, are also in the running for roles.

Trump also said on Thursday that he would name North Dakota governor Doug Burgum as secretary of the interior, giving the billionaire businessman a powerful role in the incoming administration’s efforts to boost domestic energy production.

Additional reporting by Gregory Meyer