The Trump administration announced on Thursday that it was laying off 10,000 employees at the Health and Human Services Department as part of a broad reorganization that reflects the priorities of the health secretary, Robert F. Kennedy Jr., and the White House’s drive to shrink the government.

The layoffs are a drastic reduction in personnel for the health department, which had employed about 82,000 people and touches the lives of every American through its oversight of medical care, food and drugs.

The layoffs and reorganization will cut especially deep at two agencies within the department that have been in Mr. Kennedy’s sights: the Food and Drug Administration and the Centers for Disease Control and Prevention. Those agencies are expected to lose roughly 20 percent of their staff members from the latest cuts alone.

Together with previous buyouts and early retirements spurred by Trump administration policies, the move will pare the health department down to about 62,000 employees, the agency said.

The restructuring is intended to bring communications and other functions directly under Mr. Kennedy. And it includes creating a new division called the Administration for a Healthy America.

“We’re going to do more with less,” Mr. Kennedy said, even as he acknowledged that it would be “a painful period for H.H.S.”

Mr. Kennedy asserted that rates of chronic disease rose under the Biden administration even as the government grew. But he did not provide data to back up his claim; experts say that rates of chronic disease have been rising for the past two decades, including under the first Trump administration. Two 2024 analyses of the issue used C.D.C. data from 2020.

The health secretary pitched the changes as a way to refocus the agency on Americans’ health, but did not outline any specifics on how he would reduce rates of diabetes, heart disease or any other conditions.

Inside the affected agencies, stunned employees struggled to absorb the news. Democrats and outside experts said the move would decimate agencies charged with protecting the health and safety of the American public, depriving it of the scientific expertise necessary to respond to current and future biological threats.

“In the middle of worsening nationwide outbreaks of bird flu and measles, not to mention a fentanyl epidemic, Trump is wrecking vital health agencies with the precision of a bull in a china shop,” said Senator Patty Murray, a Washington Democrat who has been a leader on health issues in Congress.

She called Mr. Kennedy’s comments about doing more with less an “absurd suggestion” that “defies common sense.” Her sentiments were echoed by several agency employees, who spoke on the condition of anonymity to avoid retribution.

They said they worried not for themselves, but for the country, expressing concern about what the layoffs would mean for public health and whether putting safety at risk was really what Americans wanted.

Under the plan, the C.D.C., which handles a wide range of health issues including H.I.V./AIDS, tobacco control, maternal health and the distribution of vaccines for children, would return to its “core mission” of infectious disease.

“Converting C.D.C. to an agency solely focused on infectious diseases takes us back to 1948 without realizing that in 2025, the leading causes of death are noncommunicable disease,” said Dr. Anand Parekh, who served in the health department during the Obama administration and is now the chief medical adviser at the Bipartisan Policy Center in Washington.

The C.D.C. will have its work force cut by about 2,400 employees, and will narrow its focus to “preparing for and responding to epidemics and outbreaks,” an H.H.S. fact sheet said. But it will also absorb the health department’s Administration for Strategic Preparedness and Response, which has 1,000 employees and was elevated to its own separate agency under the Biden administration during the coronavirus pandemic.

The reorganization will cut 3,500 jobs from the F.D.A., which approves and oversees the safety of a vast swath of the medications and food people eat and rely on for well-being, the fact sheet said. The cuts are said to be administrative, but some of the roles support research and monitoring of the safety and purity of food and drugs, as well as travel planning for inspectors who investigate overseas food and drug facilities.

The National Institutes of Health will lose 1,200 staff members, and the agency that administers Medicare and Medicaid is expected to lose 300.

All of those agencies tend to operate under their own authority, and Mr. Kennedy has been at odds with all of them. Mr. Kennedy assailed them, and other parts of the department, in a YouTube video.

“When I arrived, I found that over half of our employees don’t even come to work,” he claimed. “H.H.S. has more than 100 communications offices and more than 40 I.T. departments and dozens of procurement offices and nine H.R. departments. In many cases, they don’t even talk to each other. They’re mainly operating in silos.”

Mr. Kennedy’s move to take control of health communications is significant. Currently, agencies including the C.D.C., the N.I.H. and the F.D.A. manage their own communications with the press and the public.

During the first Trump administration, the C.D.C. clashed with the White House, which silenced agency scientists and took control of its public outreach about Covid-19. The agency’s chief spokesman quit in frustration last week, saying the C.D.C. has been muzzled since January, when Mr. Trump returned to office.

The 28 divisions of the Health and Human Services Department will be consolidated into 15 new divisions, according to a statement issued by the department. Mr. Kennedy announced the changes in his video. The staff cuts, reported earlier by The Wall Street Journal, are being made in line with President Trump’s order to carry out the Department of Government Efficiency’s drive to shrink the federal work force.

The plan also includes collapsing 10 regional H.H.S. offices into five.

The department notified union leaders of the “reduction in force” — known as a “RIF” in federal parlance — early Thursday morning by email. The message, obtained by The New York Times, said the layoffs would most likely take effect on May 27 and were “primarily aimed at administrative positions including human resources, information technology, procurement and finance.”

Democrats including Ms. Murray reacted with fury to the cuts. Representative Gerald E. Connolly of Virginia, the top Democrat on the Oversight and Government Reform Committee, said the cuts were troubling amid a bird flu outbreak and an uptick in measles cases.

“This is a grave mistake,” Mr. Connolly said in a statement, “and I have serious concerns about how this will impact Americans’ well-being now and long into the future.”

Republicans seemed to be taking more of a wait-and-see stance. Senator Bill Cassidy, Republican of Louisiana and the chairman of the committee that oversees health, said he had breakfast with Mr. Kennedy on Thursday. Mr. Cassidy suggested he was open to the reorganization but expected the two “would have more conversations” about specific cuts as their effects became clearer.

Doreen Greenwald, the president of the National Treasury Employees Union, which represents 18,500 H.H.S. staff members across the country, issued a statement vowing to “pursue every opportunity to fight back on behalf of these dedicated civil servants.”

“The administration’s claims that such deep cuts to the Food and Drug Administration and other critical H.H.S. offices won’t be harmful are preposterous,” Ms. Greenwald said.

Xavier Becerra, who served as health secretary under President Joseph R. Biden Jr., issued a statement saying the cuts would most likely downgrade services to elderly and disabled people, and those with mental health challenges, in addition to preparedness for health crises.

“This has the makings of a man-made disaster,” he said on social media.

Mr. Kennedy suggested in the video that the changes would help his team get more access to data. That prospect has been worrisome to his critics, given Mr. Kennedy’s long history of manipulating figures to advance arguments about what he contends are the risks of vaccines that have widely been deemed safe.

“In one case,” Mr. Kennedy said, “defiant bureaucrats impeded the secretary’s office from accessing the closely guarded databases that might reveal the dangers of certain drugs and medical interventions.”

Mr. Kennedy said the new division he is creating, the Administration for a Healthy America, would combine a number of agencies focused on substance abuse treatment and chemical safety, as well as the agency that administers courts that handle federal claims over vaccine injuries.

“We’re going to consolidate all of these departments and make them accountable to you, the American taxpayer and the American patient,” he said. “These goals will honor the aspirations of the vast majority of existing H.H.S. employees who actually yearn to make America healthy.”

Michael Gold contributed reporting.