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.

“The revolution begins today!” Health Secretary Robert F. Kennedy Jr. wrote on social media as he celebrated the swearing-in of his latest hires: Dr. Jay Bhattacharya, the new director of the National Institutes of Health and Martin Makary, the new Food and Drug Administration commissioner. Kennedy’s post came just hours after employees began receiving emailed layoff notices. He later wrote, “Our hearts go out to those who have lost their jobs,” but said that the department needs to be “recalibrated” to emphasize disease prevention.

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.

HHS said layoffs are expected to save $1.8 billion annually — about 0.1% — from the department’s $1.7 trillion budget, most of which is spent on Medicare and Medicaid health insurance coverage for millions of Americans.

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.

Some staffers began getting termination notices in their work inboxes at 5 a.m., while others found out their jobs had been eliminated after standing in long lines outside offices in Washington, Maryland and Atlanta to see if their badges still worked.

Some 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. Adding to the confusion, some layoff notices included instructions to file equal employment complaints to a person who had died in November.

At the NIH, 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 that 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 least nine high-level CDC directors were placed on leave and were also offered reassignments to the Indian Health Service. Some public health experts outside the agency saw it as a bid to get veteran agency leaders to resign.

At CDC, union officials said programs were eliminated because of the layoffs focused on smoking, lead poisoning, gun violence, asthma and air quality, and occupational safety and health. The entire office that handles Freedom of Information Act requests was shuttered. Infectious disease programs took a hit, too, including programs that fight outbreaks in other countries and labs focused on HIV and hepatitis in the U.S. and staff trying to eliminate tuberculosis.

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.

“Congress and citizens must join us in pushing back,” said Everett Kelley, president of the American Federation of Government Employees. “Our health, safety, and security depend on a strong, fully staffed public health system.”

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 intent of cuts to the CDC 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.

Cuts were less drastic at the Centers for Medicare and Medicaid Services, where Trump’s Republican 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.

However, the impact will still be felt, with the department slashing much of the workforce at the Office of Minority Health.

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.

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.

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, the world’s leading medical research agency.
• 300 jobs at the CMS, which oversees the Affordable Care Act marketplace, Medicare and Medicaid.