The agency has lost its independence and nearly a third of its staff, as Health Secretary Robert F. Kennedy Jr. and associates have tightened control.

For decades, the Centers for Disease Control and Prevention was the undisputed global leader in public health. Its scientists helped train health officials worldwide. In the United States, it was the primary source of guidance for prevention and treatment of diseases, including diabetes, H.I.V. and the seasonal flu.

But after a year and a half in the cross hairs of Health Secretary Robert F. Kennedy Jr.’s drive to remake public health policy, the agency is a skeleton of the powerhouse it was.

The Trump administration’s widespread layoffs in early 2025 cut 18 percent of the C.D.C.’s staff. But new personnel data, compiled by a group of former federal scientists and reported here for the first time, indicate that the agency’s staff has dwindled far more, as large numbers of employees retired or resigned. As of May 2026, the C.D.C. had 30 percent fewer employees than it did before the layoffs, the data show.

Interviews with more than 30 current and former employees reveal the agency is now tightly controlled by Mr. Kennedy and his associates, and its scientists are finding it increasingly difficult to do their jobs effectively. (Some of them spoke on the condition of anonymity because of a fear of retaliation from the administration.) The changes have hindered the C.D.C.’s ability to respond to outbreaks as measles spreads at home and Ebola abroad, and to issue timely guidance on vaccinations as cooling temperatures kick off the respiratory season, according to current and former employees. State and local health departments, which rely on the C.D.C. for resources and technical advice, have been stymied by delays. Entire divisions have been shuttered, including teams that worked on smoking, sexual violence, child abuse and falls among older adults.

Even some areas central to the Trump administration’s priorities have been gutted. Despite Mr. Kennedy’s focus on chronic diseases and autism, the C.D.C. centers that aim to prevent chronic diseases and birth defects are at half their previous size, according to the new data, compiled by the Public Data Observatory from the Office of Personnel Management, the Department of Health and Human Services, and the employee union.

The layoffs spared the agency’s infectious disease centers. But even so, the center for emerging and zoonotic diseases, which manages Ebola and hantavirus, among others, now has nearly 300 fewer employees than in March 2025, and the respiratory disease center has lost nearly 200 — about 17 percent in each case.

Beyond staff reductions, there is a leadership vacuum. Only one of the 11 center directors from March 2025 remains at the agency. Most of the other centers are being run by acting directors, some of whom were elevated from jobs one or two levels below.

“It’s a zombified C.D.C. where you have all the bits and pieces — like the body’s there, the substance is there, but it’s not acting like how an agency like that should act,” said Dr. Demetre Daskalakis, who led the respiratory disease center before he resigned in August 2025.

Despite a series of high-profile disease outbreaks, C.D.C. workers have had little contact with the World Health Organization, with members of Congress and even, for a time, with their partners in state and local health departments, some employees said. Statements to the media about health crises are also tightly controlled by H.H.S.

Even basic functions have broken down. Travel approvals take months; upkeep of bathrooms and vacuuming of offices have been disrupted, some current employees said.

One senior official said it felt as though the agency was being held together with bubble gum and duct tape, with employees running from crisis to crisis, and nothing working the way it is supposed to.

The Department of Health and Human Services did not respond to a series of questions about the C.D.C.’s work, staffing and independence. “C.D.C. continues to protect the health and safety of the American people and communicate clearly about the importance of vaccination,” the department said in an emailed statement.

But several former officials disagreed with that assessment, noting that the C.D.C. has offered little leadership or clear communication even as, in just a few months, the nation has grappled with record cases of measles, cyclosporiasis and rabies.

“Imagine losing a third of a city’s firefighters and then wondering why downtown is burning,” said Dr. Jonathan Mermin, who led the agency’s center for H.I.V. and sexually transmitted infections till April 2025, and is now the dean of the Columbia University Mailman School of Public Health.

Political Interference From the very first day of Mr. Trump’s second term, when he withdrew the country from the W.H.O., his administration has sought to upend the nation’s health policies and align them with his political priorities.

In past administrations, just two or three political appointees had purview over the C.D.C. Now, there are nearly 20 political appointees from H.H.S. who communicate with C.D.C. staff members, sometimes directing them to spend time and funding on dubious theories outside the agency’s scope, according to several officials.

Last year, an H.H.S. official directed the C.D.C. to award a no-bid contract — a rarity for the agency — to Rensselaer Polytechnic Institute to explore whether immunizing pregnant women would lead to autism in their children, a theory that Mr. Kennedy has espoused but that has been debunked by numerous studies. To pay for the research, the C.D.C. took $362,000 from a program that provides free vaccines to about half of American children.

In an email viewed by The New York Times, Stuart Burns, a political appointee, asked C.D.C. employees to pull together details of every measles case since 2010, including patients’ underlying medical conditions with diagnostic codes; that information is not collected routinely, they told him. Mr. Kennedy has falsely argued that measles only causes death in children who are already ill with other conditions.

Dr. William “Reyn” Archer III, another appointee who previously oversaw the C.D.C., repeatedly asked agency employees to work on screwworm, a disease that mostly affects cattle, even though the C.D.C.’s mission is to protect human health, said Dr. Daniel Jernigan, who headed the agency’s emerging disease center before resigning in August 2025. Dr. Archer did not respond to a request for comment.

Mr. Kennedy’s associates outside the administration have also been allowed direct access to senior C.D.C. staff members. Dr. Ben Edwards, a physician in Lubbock, Texas, who treated children while he was infected with measles and whom Mr. Kennedy had praised as an “extraordinary” healer, asked senior C.D.C. officials to look into cod liver oil as a treatment for measles, citing “historical references dating back to the 1700s,” in an email viewed by The Times.

“We just would have to run around constantly to be responsive to all of these strange asks,” recalled Dr. Daskalakis, the former head of the respiratory disease center.

Numerous other instances of political interference in the C.D.C.’s activities have already been reported. Most notably, Mr. Kennedy openly overruled the C.D.C.’s scientists in imposing strict quarantine measures for people exposed to hantavirus. Dr. Jay Bhattacharya, who led the agency for six months in the absence of a Senate-confirmed director, squashed publication of a study on the effectiveness of Covid vaccines.

Some observers had hoped the C.D.C.’s new director, Dr. Erica Schwartz, a physician who has pledged to “follow the science,” would provide a bulwark against political interference. But one month into the job, she has made no public statements about the importance of childhood vaccines or corrected misinformation from her boss, Mr. Kennedy. In one of her first big decisions, she ordered agency employees to challenge Pennsylvania’s announcement of two measles deaths, shunning standard procedure.

In its statement, H.H.S. said, “Dr. Schwartz and C.D.C.’s new leadership are evaluating the agency’s structure and operations to ensure C.D.C. can effectively advance the priorities of President Trump and Secretary Kennedy and fulfill its core public health mission.” Delays and Dysfunction Across the C.D.C., the employees who remain are backfilling roles left vacant.

“I’ve never seen such a plethora of acting roles in my life,” the agency’s new chief operating officer, Sean Slovenski, acknowledged to staff members at a meeting in June, a recording of which was obtained by The Times.

Many divisions are struggling to disburse money appropriated by Congress. In an email in May viewed by The Times, an official asked for volunteers from other offices to help the Division of Population Health, which had lost 88 percent of its staff, write notices of funding opportunities for diseases like lupus and epilepsy.

“We are overseeing millions of dollars in funded work, but how can we do this in a responsible way when we just don’t have enough people to really oversee the work well?” said one official at the agency’s chronic disease center.

The agency’s dysfunction is alarming public health experts even outside the country, who had long relied on the C.D.C.’s expertise during global crises. At a recent meeting of global flu experts, Dr. Jernigan said, “people truly believe that we are less prepared now and less capable of having a coordinated response than we were before the pandemic.” By this time of year in 2024, the C.D.C. had published detailed recommendations for vaccines against respiratory diseases, with endorsements from the director at the time, Dr. Mandy Cohen, and notes from a meeting of its vaccine advisers.

But because of a federal court ruling, the C.D.C.’s vaccine advisers have not met since December, and the agency has not issued updated recommendations for the vaccines. Some employees at the agency wanted to post clear recommendations for flu vaccines, but did not want to get into a conflict with political appointees, Dr. Jernigan said.

After controversy erupted over the Covid vaccine study, Dr. Bhattacharya demoted the previous acting director of the respiratory disease center, Dr. Brandi Limbago, and replaced her with Rebecca Greco Koné, an operational leader who is not a scientist.

The lack of experienced staff members is also affecting one of the C.D.C.’s primary functions: helping state and local governments.

The C.D.C.’s public health infrastructure grant, which helps health departments train employees and build systems, was managed by 20 project officers but it now has just three. As a result, the team’s response time for requests from local departments has increased from less than a day to more than 10, and some requests have been missed entirely. One county health department requested help on Aug. 7 with submitting data for its annual report but as of Sept. 21, the request was unanswered.

“We’re seeing a movement away from clinical guidance, from data, and from working with states,” said Dr. Debra Houry, who was the agency’s chief medical officer before resigning in August 2025.

In all, more than 1,200 people retired between March 2025 and May 2026, nearly four times the number in the comparable period in 2023-24. About 270 people are still on administrative leave, being paid but not working, while a lawsuit challenging the layoffs makes its way through the courts.

Aaron Sussell, an epidemiologist in the agency’s office in Spokane, Wash., who studied the health of miners, was placed on administrative leave in April 2025. He and his colleagues were suddenly recalled to work in January with 24 hours’ notice but by then, some had moved out of state and others had taken jobs outside the government.

Dr. Sussell, who worked at the C.D.C. for 37 years, decided to retire at the end of February. He would normally have trained his replacement. Instead, he saw an ad for his job go up five months after he left, then get taken down. His position remains unfilled.

The agency’s global health center was approved to fill 18 critical positions. Officials posted ads, interviewed candidates and made job offers to some. But the offers expired before H.H.S. completed the next steps like background checks, so they had to start the interview process all over again, according to an official with knowledge of the situation.

By law, C.D.C. employees who were laid off have priority to be rehired, but some applicants were told they were ineligible for the very jobs they had previously held for years. In all, the agency hired 108 employees between March 2025 and May 2026, compared with more than 1,500 between March 2023 and May 2024.

The staffing totals do not always tell the full story. One C.D.C. branch that works on vaccine-preventable diseases, such as measles, has lost only seven of its 50 people. But they include the four most experienced scientists from the measles lab team, which is trying to analyze genetic material that will determine whether the United States can still claim to have eliminated measles. And funding cuts to other federal agencies have also affected the C.D.C.’s budget for fighting infectious diseases: The budget for a branch that tackles Ebola and other deadly diseases has dropped by 36 percent.

Some C.D.C. scientists are hesitant to sign up for the Ebola response in the Democratic Republic of Congo because they disagree with the administration’s focus on keeping infected people out of the country rather than on helping to contain the outbreak.

Others are too overburdened to help. About 100 C.D.C. staff members have been deployed to Congo to help with the outbreak, compared with about 2,000 who went to West African countries during the 2014 Ebola outbreak.

“If you’re doing your job and your boss’s job who left, and you also have three staff people who left under you,” said Dr. Fiona Havers, who resigned from the C.D.C. in June 2025, “no one has the spare capacity to help out in something that’s not in their field.” Apoorva Mandavilli reports on science and global health for The Times, with a focus on infectious diseases and pandemics and the public health agencies that try to manage them.