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.

The Trump administration laid off thousands of federal health workers on Tuesday in a purge that included senior leaders and top scientists charged with regulating food and drugs, protecting Americans from disease and researching new treatments and cures.

Layoff notices began arriving at 5 a.m., workers said, affecting offices responsible for everything from global health to food safety. Senior officials based in the Washington area and Atlanta were reassigned to the Indian Health Service and asked to choose among locations including Alaska, Oklahoma and New Mexico — a tactic to force people out, employees said.

The layoffs and reassignments touch every aspect of the federal Department of Health and Human Services, and are part of what the administration has said is a vast restructuring of the agency. Entire units focused on reproductive health and preventing gun injuries were wiped out. So was a vaccine research program aimed at preventing the next pandemic.

On Tuesday afternoon, Senator Bill Cassidy, Republican of Louisiana and chairman of the Senate health committee, summoned Health Secretary Robert F. Kennedy Jr. to testify about the agency reorganization at a hearing on April 10.

Outside experts and former officials said the loss of expertise was immeasurable. Many described it as a “bloodletting.” Hundreds of people, many carrying handmade signs, gathered in the lobby of a National Cancer Institute building in the Maryland suburbs on Tuesday morning to witness the exodus of fired workers, but were dispersed so they could walk out without fanfare. Some employees, both current and former, were in tears.

But as staff members reeled and comforted one another, Mr. Kennedy posted a video on social media that showed him swearing in the new heads of the Food and Drug Administration, Dr. Martin A. Makary, and the National Institutes of Health, Dr. Jay Bhattacharya.

“Welcome aboard,” Mr. Kennedy said. “The revolution begins today.”

The cuts were intended to fulfill Mr. Kennedy’s plan, announced last week, to shrink his department from 82,000 to 62,000 employees. Tuesday’s layoffs affected 10,000 employees, on top of 10,000 who had already been fired or left voluntarily. The department did not respond to a request for comment on the record.

The restructuring is intended to bring communications and other functions directly under Mr. Kennedy, who has vowed to “make America healthy again.” It includes collapsing a number of agencies into a new division called the Administration for a Healthy America. Mr. Kennedy said last week that the department was “going to do more with less.”

Jessica C. Henry, 40, said she had been fired along with her entire team of communications and health education specialists at the National Institute of Dental and Craniofacial Research, a small branch of the National Institutes of Health with a budget of about $500 million. Their work focused on educating people about childhood dental health, including birth defects like cleft lips and palate, as well as water fluoridation and instructions on oral health maintenance as an aging adult.

Ms. Henry said she logged into her computer at her desk at N.I.H. headquarters in Maryland around 7 a.m., only to see an email notifying her of her termination.

“I also just feel so confused, and honestly kind of angry, because we hear a lot about how the administration wants to increase transparency,” she said in an emotional interview. “They want accountability to the American people for how their tax dollars are being spent. And from what I can tell, they just fired all of us who do that.”

Layoff notices began arriving at 5 a.m., workers said, affecting offices responsible for everything from global health to medical devices to communications at agencies including the F.D.A., the N.I.H. and the Centers for Disease Control and Prevention.

Mr. Kennedy is also eliminating entire but lesser known parts of his department, such as the Administration for Community Living, which supports programs that help older Americans and people with disabilities live independently. Advocates for disability rights say the cuts could deprive the most vulnerable Americans of housing, personal care and other services.

At the Substance Abuse and Mental Health Services Administration, cuts hollowed out entire offices including the internal policy lab, the team that administers a national survey of drug use, an office of behavioral health equity, the contracts management division and all 10 regional offices, according to Miriam Delphin-Rittmon, the former assistant health secretary for mental health and substance use. She left the agency on Jan. 20 and has been hearing from former colleagues.

The policy lab was established as part of the 21st Century Cures Act, a law passed by Congress in 2016.

“It’s not clear really the strategy,” Ms. Delphin-Rittmon said. “Those are important content areas.”

The cuts also fell on senior leaders, including the director of the center for mental health services, Dr. Anita Everett, who was hired into a senior position at the agency during the first Trump administration, and Michelle Greenhalgh, the agency’s director of legislative affairs, according to multiple people with direct knowledge of the filings.

“Today was simply a tragedy,” said Michael T. Osterholm, who directs the University of Minnesota’s Center for Infectious Disease Research and Policy, and has advised presidents of both parties. “There is so much intellectual capital that literally got swept under the rug today in this country, and we are going to pay a price for this for years to come.”

Dr. Bhattacharya, on his first day of work, sent an email to staff saying the layoffs would “have a profound impact on key N.I.H. administrative functions, including communications, legislative affairs, procurement and human resources.” He expressed his appreciation for the “scientists and staff whose work has contributed to lifesaving breakthroughs in biology and medicine.”

A number of top health officials received notice that they were being reassigned to regional offices of the Indian Health Service, which is responsible for providing federal health services to Native Americans and Alaska Natives.

At N.I.H., several institute directors — including Dr. Jeanne Marrazzo, head of the National Institute of Allergy and Infectious Diseases, the institute formerly led by Dr. Anthony S. Fauci — were reassigned. So were Dr. Fauci’s wife, Christine Grady, the head of the N.I.H. Office of Bioethics, and Dr. Clifford Lane, a close ally of Dr. Fauci’s who oversaw clinical research.

At the F.D.A., the top tobacco regulator, Brian King, was reassigned. At the C.D.C., several leaders, including Kayla Laserson, who ran the global health center, also were reassigned to the Indian Health Service.

The health service is chronically understaffed and underfunded; the reassignment notices said it has an “untenable vacancy rate” of 30 percent. Mr. Kennedy recently lamented that it has been “treated as the redheaded stepchild at H.H.S.” and said President Trump wants him to “rectify this sad history.”

Those who received the reassignments were given until Wednesday to decide whether to accept the offer, or leave their jobs.

Some workers knew that they would be affected by the layoffs. At the department headquarters in Washington, officials responsible for minority health and infectious disease prevention were told Friday that their offices were being eliminated, according to employees.

Others were caught off guard. At the F.D.A., senior leaders were pushed out and offices focused on food, drug and medical device policy were hit with deep staff reductions amounting to about 3,500 agency staff members. On Friday, the agency’s top vaccine regulator, Dr. Peter Marks, was forced to resign under pressure. He lashed out at Mr. Kennedy afterward, saying the secretary “doesn’t care about the truth.”

Some F.D.A. workers said that they discovered they had been fired when they attempted to scan their badges to get into the building early Tuesday. The office of the center director for veterinary medicine was wiped out, according to a person familiar with the cuts. That included veterinarians leading bird flu response for the agency.

Employees of several F.D.A. labs around the United States were also let go, including those who test medical products in Detroit and San Juan, Puerto Rico, and those who test food in San Francisco and Chicago.

“The F.D.A. 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,” Dr. Robert Califf, who ran the Food and Drug Administration during the Biden administration, wrote on social media. He said “history will see this” as “a huge mistake.”

At the C.D.C., which Mr. Kennedy wants to pare back to focus only on infectious disease, the reorganization is likely to have immediate effects. Offices devoted to the study of other programs, including reproductive health, chronic disease and gun violence prevention, were disbanded.

The administration has eliminated offices dedicated to protecting workers in various industries, including those that inspect mines for safety. A two-year project to study the effects of radiation was eliminated, as was an ongoing project on lead contamination in Milwaukee.

“These cuts to agency experts and programs leave our country less safe, less prepared and without the necessary talent and resources to respond to health threats,” Dr. Mandy Cohen, who led the Centers for Disease Control and Prevention during the Biden administration, said in a text message.

Some infectious disease teams were also laid off. A group focused on improving access to vaccines among underserved communities was cut, as was a group of global health researchers who were working on preventing transmission of H.I.V. from mother to child.

H.I.V. prevention was a big target overall. The Trump administration had been weighing moving the C.D.C.’s division of H.I.V. prevention 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.

Employees laid off at the agency included those studying injuries, asthma, lead poisoning, smoking and radiation damage, as well as those that assess the health effects of extreme heat and wildfires.

Communications offices were hit particularly hard across agencies including the N.I.H., C.D.C. and F.D.A. Renate Myles, the communications director at the National Institutes of Health, received a notice of reassignment. At the C.D.C., specialists in tuberculosis communications and education were laid off.

Mr. Kennedy, who promised “radical transparency,” has said he wants to consolidate communications under his purview.

The H.H.S. “is centralizing communications across the department to ensure a more coordinated and effective response to public health challenges, ultimately benefiting the American taxpayer,” Emily Hilliard, deputy press secretary for the department, said in an email on Friday.

But other divisions responsible for providing the public with information were hit, too.

The team that responds to Freedom of Information Act requests at the C.D.C. was eliminated, and a similar team at the F.D.A. was deeply cut, according to sources familiar with each office. They spoke on condition of anonymity out of fear of reprisal.

Processing such requests is required by law, but can be a painstaking process, given rules requiring the redaction of information such as a company’s trade secrets.

Benjamin Mueller, Gina Kolata, Aishvarya Kavi and Margot Sanger-Katz contributed reporting.