President-elect Donald Trump said Thursday that he would nominate Robert F. Kennedy Jr. to lead the Department of Health and Human Services — setting up a debate over whether Kennedy, whose vaccine skepticism and unorthodox views about medicine make public health officials deeply uneasy, can be confirmed.

Trump is stocking his administration with people whom even some Republicans find alarming, including former Rep. Matt Gaetz as attorney general and Pete Hegseth, a Fox News host, as defense secretary. In choosing Kennedy, Trump is picking someone who is at war with the very public health agencies he would oversee.

“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 on Truth Social, his social media platform, in making the announcement.

“Mr. Kennedy,” he added, “will 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!”

Public health experts were appalled. Dr. Richard Besser, the CEO of the Robert W. Johnson Foundation and a former acting director of the Centers for Disease Control and Prevention, said that having Kennedy in the health secretary’s job was “absolutely frightening” and “would pose incredible risks to the health of the nation,” because Kennedy’s assault on the nation’s public health apparatus was only worsening the mistrust lingering after the coronavirus pandemic.

“Robert F. Kennedy is part of the problem and cannot be part of the solution,” Besser said.

Some of Kennedy’s views, such as his emphasis on nutrition and removing additives from foods, are mainstream. But Kennedy has spread false information about vaccines, including that they cause autism — a theory that has long been debunked. He has publicly contradicted the CDC’s recommendation that communities fluoridate their water to guard against tooth decay.

He has embraced raw milk, despite the Food and Drug Administration’s warning that drinking it is risky, particularly amid a current bird flu epidemic among dairy cows. And he has promoted hydroxychloroquine, a drug whose emergency authorization as a COVID-19 treatment was revoked by the FDA after a study of 821 people found it lacked effectiveness.

Whether the Senate, even one controlled by Republicans, will confirm Kennedy is an open question. In addition to his outside-the-mainstream views about medicine and health, he has been associated with a number of peculiar activities, including dumping a dead bear in Central Park and supposedly decapitating a whale. In interviews before Trump’s announcement, some Republican senators said Kennedy gave them pause, but none ruled out voting for him.

“I find some of his statements to be alarming, but I’ve never even met with him or sat down with him or heard him speak at length,” said Sen. Susan Collins, R-Maine, a centrist whose vote could be critical to Kennedy’s confirmation prospects. “So I don’t want to prejudge based just on press clippings that I have read.” However, she added, “I think it would be a surprising choice.”

But Republicans more closely aligned with Trump were enthusiastic.

“One hundred percent,” Sen. Tommy Tuberville, R-Ala., a member of the Senate health committee, said when asked if he would vote to confirm Kennedy. Tuberville said he was a fan of Kennedy’s because of the work he had done with food and vaccines, adding, “More than anybody that I know of, he’s had an open mind.”

The strange political marriage between Trump and Kennedy, who endorsed Trump after suspending his presidential campaign, has been beneficial for both men. The merger gave Kennedy a platform he previously lacked — slickly produced rallies and roaring crowds.

But Kennedy gave Trump something as well — a core of new supporters, in particular, disaffected Democrats and “crunchy granola moms” who might not have otherwise voted for a felon with strongman tendencies. Trump grew impressed with Kennedy, and vowed to let him go “wild on health.”

Kennedy has lately shifted his rhetoric away from vaccines and toward ending what he calls the “chronic disease epidemic,” a goal that public health experts say is laudable. If he puts nutrition at the top of his agenda, he might find common cause with scientists and public health officials.

“I think there’s interest amongst policymakers on food,” said Dr. Anand Parekh, chief medical officer at the Bipartisan Policy Center. Parekh said he had been “pleasantly surprised” to see Kennedy emphasizing nutrition and “veering off his usual vaccine and environmental health narrow lanes.”

Kennedy has said little about health care delivery programs, such as Medicare and Medicaid, that fall within the purview of the Department of Health and Human Services. Instead, he has taken aim at regulators and public health and research agencies: the FDA, the CDC and the National Institutes of Health.

Days before the election, in a social media post that has received 6.5 million views, Kennedy threatened to fire FDA employees who have waged a “war on public health.” He listed some of the products that he claimed the agency had subjected to “aggressive suppression,” including ivermectin, raw milk and vitamins. His message to agency officials, he said, was “1. Preserve your records, and 2. Pack your bags.”