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

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

In a statement on Truth Social, his social media platform, Mr. Trump said Mr. Kennedy would restore the nation’s health 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!”

Mr. Kennedy, who has railed against the revolving door between industry and government, vowed on social media 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.”

If he is confirmed, Mr. Kennedy would have sweeping control of a department with 80,000 employees across 13 operating divisions that run more than 100 programs. Its agencies regulate the food and medicine that Americans encounter in their daily lives, decide whether Medicare and Medicaid will pay for drugs and hospital treatments, guard against infectious disease, and conduct billions of dollars of medical research into diseases like cancer and Alzheimer’s.

Many Democrats and public health experts were appalled by Mr. Trump’s selection. Dr. Richard E. Besser, the chief executive of the Robert Wood Johnson Foundation and a former acting director of the C.D.C., said that having Mr. Kennedy in the health secretary job “would pose incredible risks to the health of the nation,” because Mr. Kennedy’s assault on the nation’s public health apparatus was worsening the mistrust lingering after the coronavirus pandemic.

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