The cuts include researchers, scientists, doctors, support staff and senior leaders, leaving the federal government without many of the key experts who have long guided U.S. decisions on medical research, drug approvals and other issues.

At the National Institutes of Health, the world’s leading health and medical agency, the layoffs occurred as its new director, Dr. Jay Bhattacharya, began his first day of work. “The revolution begins today!” Health Secretary Robert F. Kennedy Jr. wrote on social media as he celebrated the swearing-in of his latest hires: Bhattacharya and Martin Makary, the new Food and Drug Administration commissioner. Kennedy’s post came just hours after employees began receiving emailed layoff notices.

Kennedy announced a plan last week to remake the department, which, through its agencies, is responsible for tracking health trends and disease outbreaks, conducting and funding medical research, and monitoring the safety of food and medicine, as well as for administering health insurance programs for nearly half the country.

The plan would consolidate agencies that oversee billions of dollars for addiction services and community health centers under a new office called the Administration for a Healthy America.

The layoffs are expected to shrink HHS to 62,000 positions, lopping off nearly a quarter of its staff — 10,000 jobs through layoffs and another 10,000 workers who took early retirement and voluntary separation offers. Many of the jobs are based in the Washington area, but also in Atlanta, where the U.S. Centers for Disease Control and Prevention is based, and in smaller offices throughout the country.

Two lines with hundreds of employees wrapped around the HHS headquarters building Tuesday morning. Workers waited in the chilly spring weather to be individually scanned in for access to the building. Some said they were waiting to find out if they still had jobs. Others gathered at local coffee shops and lunch spots after being turned away, finding out they had been eliminated after decades of service.

One wondered aloud if it was a cruel April Fools’ Day joke.

At the NIH, the cuts included at least four directors of the NIH’s 27 institutes and centers who were put on administrative leave, and nearly entire communications staffs were terminated, according to an agency senior leader, speaking on the condition of anonymity to avoid retribution.

An email viewed by The Associated Press shows some senior-level employees of the Bethesda, Maryland, campus who were placed on leave were offered a possible transfer to the Indian Health Service in locations including Alaska and given until the end of Wednesday to respond.

At the FDA, dozens of staffers who regulate drugs, food, medical devices and tobacco products received notices, including the entire office responsible for drafting new regulations for electronic cigarettes and other tobacco products. The notices came as the FDA’s tobacco chief was removed from his position. Elsewhere at the agency, more than a dozen press officers and communications supervisors were notified that their jobs would be eliminated.

“The FDA as we’ve known it is finished, with most of the leaders with institutional knowledge and a deep understanding of product development and safety no longer employed,” said former FDA Commissioner Robert Califf in an online post. Califf stepped down at the end of the Biden administration.

The layoff notices came just days after President Donald Trump moved to strip workers of their collective bargaining rights at HHS and other agencies throughout the government.

Democratic Sen. Patty Murray of Washington predicted the cuts will have ramifications when natural disasters strike or infectious diseases, like the ongoing measles outbreak, spread.

“They may as well be renaming it the Department of Disease because their plan is putting lives in serious jeopardy,” Murray said Friday.

The CDC has not provided a breakdown of cuts, but employees in different parts of the organization described to the AP extensive layoffs in programs that track asthma, air pollution, smoking, gun violence, reproductive health, climate change and other health threats.

The intent seems to be to create “a much smaller, infectious disease agency,” but it is destroying a wide array of work and collaborations that have enabled local and national governments to be able to prevent deaths and respond to emergencies, said Dr. Georges Benjamin, executive director of the American Public Health Association.

Dr. Tom Frieden, the CDC’s director during President Barack Obama’s administration, said he is particularly concerned about cuts to the CDC’s Office on Smoking and Health and the agency’s Global Health Center.

“Weakening tobacco prevention is a gift to Big Tobacco that would guarantee more addiction, disease, and death,” Frieden said, while cuts to the CDC’s global disease detection work will cost lives.

Among the hardest-hit centers was the CDC’s National Institute for Occupational Safety and Health, with more than 1,000 employees. NIOSH is based in Cincinnati but also has people in Pittsburgh; Spokane, Washington; and Morgantown, West Virginia.

Cuts were less drastic at the Centers for Medicare and Medicaid Services, where the Trump administration wants to avoid the appearance of debilitating the health insurance programs that cover roughly half of Americans, many of them poor, disabled and elderly.

But the impact will still be felt, with the department slashing much of the workforce at the Office of Minority Health, which no longer has a functioning webpage.

Jeffrey Grant, a former CMS deputy director, said the office is not part of a diversity, equity and inclusion program, the kind Trump’s Republican administration has sought to end.

“This is not a DEI initiative. This is meeting people where they are and meeting their specific health needs,” said Grant, who resigned last month and now helps place laid-off CMS employees into new jobs.

The Office of Program Operations & Local Engagement, which does local outreach for CMS operations, was also gutted, Grant said.

Beyond layoffs at federal health agencies, cuts are beginning at state and local health departments as a result of an HHS move last week to pull back more than $11 billion in COVID-19-related money. Some health departments have identified hundreds of jobs that stand to be eliminated, “some of them overnight, some of them are already gone,” said Lori Tremmel Freeman, chief executive of the National Association of County and City Health Officials.

A coalition of state attorneys general sued the Trump administration on Tuesday, arguing the cuts are illegal, would reverse progress on the opioid crisis and would throw mental health systems into chaos.

Kennedy criticized the department he oversees as an inefficient “sprawling bureaucracy” in a video Thursday announcing the restructuring. He said the department’s $1.7 trillion yearly budget “has failed to improve the health of Americans.”

“I want to promise you now that we’re going to do more with less,” Kennedy said.

HHS has not provided additional details or comments about Tuesday’s mass firings, but on Thursday it provided a breakdown of some of the cuts.

• 3,500 jobs at the FDA, which inspects and sets safety standards for medications, medical devices and foods.
• 2,400 jobs at the CDC, which monitors for infectious disease outbreaks and works with public health agencies nationwide.
• 1,200 jobs at the NIH.
• 300 jobs at the Centers for Medicare and Medicaid Services, which oversees the Affordable Care Act marketplace, Medicare and Medicaid.

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Associated Press writers Lauran Neergaard, Amanda Seitz and Matthew Perrone in Washington and Mike Stobbe in New York contributed.