CDC, NIH and more health agencies brace for layoffs with DOGE and RFK Jr.’s restructuring. Here’s what we know.

Officials at agencies throughout the Department of Health and Human Services say they are bracing for steep layoffs, as Secretary Robert F. Kennedy Jr. and his aides are nearing their final decisions on a sweeping restructuring of the department.

Decisions by Kennedy and his team on the changes to the department’s makeup and organization are expected within a week or two, multiple senior health officials have been told. One official said aides have begun drafting a reorganization announcement.

The department did not respond to a request for comment. 

In addition to the formal head of the White House’s Department of Government Efficiency team, Amy Gleason, several other members of DOGE are HHS employees. Some have been intimately involved with the plans, including former insurance executive Brad Smith, who was a top Medicare and Medicaid official during the first Trump administration.

The expected cuts at the department under the reorganization and “reduction-in-force” plans ordered by the White House come after many workers have already been fired or let go throughout the nation’s health agencies through other moves, like earlier attempts to purge thousands of probationary workers, end fellowship programs and terminate contractor agreements.

Here is the latest we know about the reorganization at several agencies within HHS, based on conversations with more than a dozen health officials who were not authorized to speak publicly.

Agency for Healthcare Research and Quality

Workforce cuts laid out by the HHS and DOGE officials for some senior leaders have been unprecedented. In one agency within HHS, the Agency for Healthcare Research and Quality, DOGE officials told leaders on March 11 to expect up to 90% of their staff to be cut.

The agency has around 300 employees, many tasked with collecting and analyzing some of the federal government’s most widely cited metrics on health care, including decades-old datasets tracking hospitalizations and emergency room visits nationwide that economists and health policy researchers rely on. 

AHRQ also works on a number of programs funded by Congress to address patient safety and health care mishaps, like a program aimed at combating antibiotic resistant bacteria.

“The current staff is about 45 highly skilled economists and statisticians. DOGE wants that cut to six total staff. The six people who would be willing to stay under those conditions would not exactly be the best,” one health official told CBS News of cuts to one of the agency’s teams overseeing a large federal database on medical spending.

Centers for Disease Control and Prevention

At the Centers for Disease Control and Prevention, some managers have been told to expect cuts handed down from the department that could result in up to 30% of the Atlanta-based agency’s staff being let go. 

Close to 12,820 people were employed by the CDC at the end of the last fiscal year, federal records show, up from 10,487 during the final year of the first Trump administration.

“A 30% cut would be devastating. We are already understaffed in a number of key areas and the staff that are just barely holding it together have been in various stages of burnout for five years,” one CDC official said. 

Some of those cuts might be achieved through employees who are leaving voluntarily. Managers at the agency were told around 400 workers had sought early retirement and around 600 applied for a buyout, two officials said, under offers made across HHS this month. It is unclear how many workers applied for both.

Others could be achieved by rearranging the agency’s functions. One proposal being weighed by officials would move the CDC’s HIV prevention work to elsewhere in the department.

Food and Drug Administration

Unlike other health agencies, some groups of workers at the Food and Drug Administration were told they were ineligible to take up the HHS buyout offer. 

That includes reviewers of new drug applications, whose salaries are funded primarily by fees paid for by drugmakers when seeking approval, not taxpayers. 

Others at the agency have been told to prepare for layoffs. FDA managers have said to employees internally that they were out of the loop on the scale and targets of the cuts. 

DOGE officials have made multiple visits to the agency’s Maryland headquarters, one official said. Another said that DOGE officials had been asking questions around the FDA’s labs this week. 

Multiple FDA employees said they expected some of the cuts to be achieved through what they called the growing brain drain at the agency, which has been grappling with a challenging return-to-office transition that is unlikely to ease soon. Hundreds of retirement applications are being processed at the agency, one employee said.

Far more staff work for the FDA than its headquarters is equipped to house, the employees said, leaving them scrambling for spots in overflowing parking lots and offices and running out of toilet paper in crowded bathrooms.

National Institutes of Health 

From the workforce at the National Institutes of Health, officials are expecting cuts back down to levels similar to what was seen at the end of the Trump administration. 

More than 21,000 people were employed by the medical science research agency at the end of the 2024 fiscal year, up from 17,705 at the end of the 2019 fiscal year. 

Like with other agencies, it’s possible some of the expected cuts could be made up for by voluntary departures of scientists and other workers. One person said they had heard in meetings that some 1,400 had sought either the buyout, early retirement or both.

One person said up to 3,800 employees could be cut from the agency’s payroll, if not more, depending on how many staff can be counted from the departures.

Centers for Medicare and Medicaid Services

Cutbacks at the Centers for Medicare and Medicaid Services could be smaller, some suspect, since the agency was already facing limits to hiring under the Biden administration.

The agency’s chief operating officer said only late last year that it could resume hiring after a turnaround in its finances, InsideHealthPolicy reported in November.

There were 6,557 employees at the Baltimore-based agency in 2024, up only slightly from the workforce of 6,074 in 2019.

One CMS official said they had heard internally that the early retirements and buyouts taken up by employees in some parts of the agency may have been enough to spare much of the agency’s remaining staff.

Substance Abuse and Mental Health Services Administration

Multiple workers within the Substance Abuse and Mental Health Services Administration say they have heard nothing from agency leadership about potential cuts.

Some are hopeful that a letter from House Democrats to Kennedy denouncing reports that half of staff from the agency could be cut might stave off steep layoffs.

The agency’s workforce, which numbered 916 workers at the end of the last fiscal year, had fallen to a low of 521 employees at the end of the first Trump administration.

The firings of probationary workers earlier this year by DOGE already resulted in more than 10% of the staff at the agency being cut, including employees working on projects related to the 988 hotline for people facing mental health crises.

contributed to this report.