The extensive layoffs of federal health workers that began on Tuesday will greatly curtail the scope and influence of the Centers for Disease Control and Prevention, the world’s premier public health agency, an outcome long sought by conservatives critical of its handling of the Covid-19 pandemic.

The reorganization of the Department of Health and Human Services shrinks the C.D.C. by 2,400 employees, or roughly 18 percent of its work force, and strips away some of its core functions.

Some Democrats in Congress described the reorganization throughout H.H.S. as flatly illegal.

“You cannot decimate and restructure H.H.S. without Congress,” said Senator Patty Murray, Democrat of Washington, and a member of the Senate health committee.

“This is not only unlawful but seriously harmful — they are putting Americans’ health and well-being on the line,” she added.

Ms. Murray noted that the Trump administration had not detailed which units are being cut at the C.D.C. and other health agencies. Robert F. Kennedy Jr., the health secretary, said last week the layoffs would affect primarily administrative functions.

But according to information gathered by The New York Times from dozens of workers, the reductions were more broadly targeted. Scientists focused on environmental health and asthma, injuries, lead poisoning, smoking and climate change were dismissed.

Researchers studying blood disorders, violence prevention and access to vaccines were let go. The agency’s center on H.I.V. and sexually transmitted diseases was among the hardest hit, losing about 27 percent of its staff.

The National Institute for Occupational Safety and Health, which makes recommendations on how to keep workers safe, was all but dissolved.

What remains is a hobbled C.D.C., with a smaller global footprint, devoting fewer resources to environmental health, occupational health and disease prevention, public health experts said.

Instead, the agency will be trained more narrowly on domestic disease outbreaks. Communications will be centralized at H.H.S. in Washington.

The department intends “to ensure a more coordinated and effective response to public health challenges, ultimately benefiting the American taxpayer,” said Emily Hilliard, deputy press secretary at the department.

“C.D.C. scientists have conducted numerous interviews on a variety of topics and will continue to do so,” she added.

Critics predicted the move would prevent scientists from speaking frankly about public health.

“American taxpayers provide the resources for C.D.C.’s specialists and have the right to hear directly from them without interference by politicians,” said Dr. Thomas R. Frieden, who led the agency from 2009 to 2017.

The sweeping reductions arrive as the nation confronts an outbreak of measles in Texas and elsewhere, a spreading bird flu epidemic on poultry and dairy farms, and a raft of new questions about public health measures like water fluoridation and school vaccine requirements.

“What we seem to be seeing is a dismantling rather than a restructuring” of the public health system, said Dr. Richard Besser, chief executive of the Robert Wood Johnson Foundation and a former acting director of the C.D.C.

On Capitol Hill, the Senate health committee, which recommended confirmation of Mr. Kennedy as secretary, scheduled a hearing on the reorganization of H.H.S., citing the possible impacts on public health.

Mr. Kennedy has described the reorganization as an effort to clean up waste and bureaucracy while promising that federal health agencies would do more to improve the health of Americans.

“We’re going to eliminate an entire alphabet soup of departments and agencies while preserving their core functions by merging them into a new organization called the Administration for a Healthy America,” the secretary said in a videotaped message announcing the layoffs.

The department did not respond to requests for more detailed information.

Society’s most vulnerable — the poor, Black, Latino and Native American people, rural Americans with less access to health care, the disabled and those at highest risk for illness — are likely to be hit hardest, experts said.

“These communities rely on public health to a larger extent than wealthy communities do,” Dr. Besser said.

For decades, public health and medical research drew support across the political spectrum.

But the C.D.C. has been in the political cross hairs since the first Trump administration, when the White House muzzled the agency’s communications, meddled with its publications and blamed its scientists for bungling the pandemic response.

In recent years, lawmakers have harshly criticized the agency’s advice on masks, lockdowns, social distancing, school closures and various other attempts to contain the pandemic, calling them economically and socially disastrous.

Project 2025, the conservative blueprint for reshaping the federal government, described the C.D.C. as “perhaps the most incompetent and arrogant” federal agency, and called on Congress to curb its powers.

Through staffing cuts, the administration reduced critical divisions of the National Center for Injury Prevention and Control, and employees studying how to prevent gun violence, child abuse and elder abuse were fired.

Injuries are the leading cause of death among Americans under 45. About 47,000 Americans are killed by firearms each year, more than half of them suicides.

But gun violence is a politically fraught topic. Pressure from the National Rifle Association and conservative politicians led to a ban on using federal funds to study gun violence for almost 25 years. Funding was restored in 2019.

The injury center studied ways to improve gun safety and promoted the use of gun locks, particularly in homes where children live.

“People think of gun violence as a question for law enforcement, but the public health approach has made a big difference,” said Dr. Mark Rosenberg, a former center director.

Most of the C.D.C.’s Division of Reproductive Health, which studies maternal health, was also shuttered. Whether some or all of its portfolio will be assumed by the new organization created by Mr. Kennedy was not clear.

Pregnant women and newborns die in the United States at a far higher rate than in other industrialized nations.

In recent years, the C.D.C. focused on stark racial health disparities that put Black American women at nearly three times the risk of dying of pregnancy complications than white women.

But the Trump administration has been defunding studies of health disparities in racial, ethnic and gender minorities, saying they do not align with the president’s executive orders ending diversity, equity and inclusion initiatives.

Mr. Kennedy said last week that the National Institute for Occupational Safety and Health, which makes recommendations for preventing work-related injuries and illnesses, would be absorbed into the health department.

But on Tuesday, most of its divisions were eliminated, among them offices dedicated to protecting workers in various industries, including mine inspectors.

Even one of the agency’s most essential functions, infectious disease research, was affected.

The Trump administration had been weighing moving the H.I.V. prevention division to a different agency within the health department.

But on Tuesday, teams leading H.I.V. surveillance and research within that division were laid off. It was unclear whether some of those functions would be recreated elsewhere. (A team in the global health center working on preventing mother-to-child transmission of H.I.V. was also cut.)

Until now, the C.D.C. provided funds to states and territories for responding to and preventing H.I.V. outbreaks. Roughly one in four new diagnoses of H.I.V. is made with agency funds.

Some H.I.V. experts warned that the move could lead to a rise in H.I.V. infections among Americans.

“H.I.V. prevention is a lot more than just giving out condoms,” said Dr. John Brooks, who served as chief medical officer for the division of H.I.V. prevention until last year. “It saves lives, averts illness and produces enormous cost savings.”

Broadly, the reorganization aligns with Mr. Kennedy’s preferred emphasis on research into chronic diseases; federal research has been far too focused on infectious diseases, he has said.

But the line between them is not always clear, said Dr. Anne Schuchat, former principal deputy director of the C.D.C. Research that seems disconnected from outbreak response may also be a key for fighting pathogens.

“For Zika, we needed experts in birth defects, entomology and vector control, virologists and environmental health experts,” she said. “Emerging threats don’t respect borders of C.D.C. organizational units.”

The reorganization risks choking the talent pipeline for public health, said Ursula Bauer, former director of the agency’s National Center for Chronic Disease Prevention and Health Promotion.

“Once you decimate an agency like C.D.C., which is full of high-caliber highly trained individuals, building back is going to be incredibly difficult,” she said.

“It will take two to three times as long to undo the damage as it took to inflict it.”

The cuts also will take a toll on the agency’s ability to gather and analyze data, which are keys to identifying trends and developing interventions, Dr. Phil Huang, director of Dallas County Health and Human Services, said at a news briefing.

“You take away those systems, and it takes away the ability to see the impact of all these cuts,” he added.

A few days ago, Robert F. Kennedy Jr., the health secretary, embarked on a media tour to defend his decision to lay off thousands of his department’s workers.

He announced a plan last week to cut 10,000 jobs, in addition to the estimated 10,000 jobs cut through retirements and buyouts in the early weeks of the Trump administration.

Mr. Kennedy had called the Health and Human Services Department “the biggest agency in government, twice the size of the Pentagon, $1.9 trillion dollars,” during an interview with NewsNation. He went on to suggest that the department was doing little to improve the health of Americans, “with all the money that was being thrown at it, with all the personnel that were being brought in.”

H.H.S. does spend more than the Department of Defense, which has a discretionary budget of about $850 billion. But according to several budget experts, the overwhelming majority of the H.H.S. department’s $1.8 trillion budget is not spent on its staff.

Spending on personnel at the federal health agencies accounts for a small fraction of its budget — less than 1 percent, according to three budget experts. That includes the staff of the Food and Drug Administration, the Centers for Disease Control and Prevention, the National Institutes of Health and others.

The overwhelming majority of the money is spent through Medicare, for the health care of people older than 65, or through Medicaid, for people with low incomes. Those funds filter out to hospitals, clinics, nursing homes, dialysis centers, pharmaceutical companies, medical device makers and Medicare Advantage private insurance plans.

Melinda Buntin, professor of health policy and economics at Johns Hopkins University, said the $17.6 billion in costs for H.H.S. employees made up less than 1 percent of the department’s budget, and has risen in line with overall spending.

“I think that most people would be surprised by what a small share of Health and Human Services spending is for personnel, both their wages and compensation and benefits,” she said, noting that it made sense in the context of the agency’s spending on care.

Bobby Kogan, senior director of federal budget policy at the Center for American Progress, a left-leaning think tank, said Mr. Kennedy’s framing was “incredibly misleading.”

“It would leave someone with a super wrong understanding of what is going on really,” Mr. Kogan said. “The only story of what’s going on in H.H.S. is that we have a huge increase in the elderly population.”

An H.H.S. spokesman said the work force reductions are meant to cut $1.8 billion a year in federal spending, and that the amount is significant.

The Administration for Children and Families, another agency within H.H.S., also spends billions of dollars on services to the public. It operates Head Start programs, foster care, Temporary Assistance for Needy Families, formerly known as welfare, and care homes for unaccompanied minors from other countries.

Chris Towner, policy director for the Committee for a Responsible Federal Budget, made his own calculation, also concluding that H.H.S. staff costs appeared to be shy of 1 percent of the department’s spending. The figure could be slightly higher, he said, given the number of health agency workers with advanced degrees.

So far, the Trump administration has talked about fraud in the federal government repeatedly — though not the type that’s long been a target in Congress. Lawmakers have repeatedly raised the idea of reeling in Medicare Advantage insurance plans, which were estimated to overcharge Medicare by tens of billions of dollars a year.