He was combative, defensive and occasionally contrite. He vehemently denied, then halfheartedly apologized for suggesting in 2024 that Black children would benefit from being “re-parented.” He shouted at Democratic senators, accusing them of “grandstanding” and “selective indignation.” He insisted he had delivered “historic wins” for the health of the American people.

In the end, after four days of testimony during seven separate congressional hearings on President Trump’s budget, Health Secretary Robert F. Kennedy Jr. walked a fine line, trying to please both his base and the White House at the same time.

If there was any takeaway from Mr. Kennedy’s Capitol Hill marathon, it was that vaccination — the topic that drove Mr. Kennedy for more than a decade and catapulted him to national prominence during the coronavirus pandemic — remains the defining issue of his tenure, even as the White House, for political reasons, tries to get him to deflect attention from it.

The measles epidemic, which began last year in Texas and has killed three Americans — the first deaths from the disease in a decade — dominated the discussion. Mr. Kennedy repeatedly defended his handling of it, but appeared to back further and further away from his past criticism of the measles vaccine.

On Wednesday, under persistent questioning, he made his strongest statement yet, saying that his department “has advised every child” to get the shot. (Notably, he did not attribute that advice to himself.)

“On the whole vaccine thing, he’s trying to backpedal and hide and duck,” said Dr. Ezekiel J. Emanuel, a vice provost and public health professor at the University of Pennsylvania, who advised Democratic presidents, including Joseph R. Biden Jr. and Barack Obama, and met with Mr. Trump.

“The White House is clearly upset because his stance is not popular,” Dr. Emanuel said. “but he has not fundamentally moved his stance on vaccines.”

Indeed, Mr. Kennedy also insisted that hygiene and sanitation — and not vaccination — were responsible for the drop in deaths from infectious diseases during the 20th century, citing a 2000 study as proof. Senator Bill Cassidy of Louisiana, the Republican chairman of the Health Committee who is also a physician and has tangled repeatedly with Mr. Kennedy on vaccines, pushed back, telling the secretary he had cited the study out of context.

Mr. Cassidy, who voted to confirm Mr. Kennedy only reluctantly — and only after the secretary made a series of promises to secure the senator’s vote — seemed irritated by Mr. Kennedy’s emphasis on chronic disease over infectious disease. Mr. Kennedy noted that three Americans died of measles over the past decade, while roughly two million die from chronic disease each year.

But after the hearing, Mr. Cassidy lamented the measles deaths, saying there should be a focus on infectious disease. “We are a first-world country, and speaking as a physician that knows this can be prevented, it grieves me,” he said. “It grieves me.”

The senator himself is walking a fine line. He is facing a tough primary election next month; Mr. Trump has endorsed his challenger, as has the Make America Healthy Again PAC, which is aligned with Mr. Kennedy. Asked by a reporter whether the secretary had lived up to the promises he made, Mr. Cassidy declined to answer. “We’ll talk later,” he said.

During the hearings, which began in the House last Thursday, Mr. Kennedy revealed that after firing or laying off close to 20,000 employees at the Department of Health and Human Services last year, he was now hiring 12,000 new workers to replace them. He told lawmakers on Tuesday that he needed to “make sure that we have people to do every job.”

The about-face was infuriating, said Elizabeth Jacobs, a professor emeritus of epidemiology from the University of Arizona and a founding member of Defend Public Health, a grass-roots group formed to push back on recent challenges to public health.

“We have lost so many exceptional scientists and other employees of H.H.S., the just decades of institutional knowledge that we have lost is absolutely devastating,” she said, adding: “The estimates are it’s going to take a decade or a generation to rebuild the massive medical science juggernaut that we once had.”

Imminent cuts to Medicaid were a potent flashpoint during Mr. Kennedy’s testimony. “There are no cuts to Medicaid!” he shouted on Wednesday to the Senate Finance Committee as Democrats insisted there were.

The sweeping domestic policy bill that Mr. Trump signed into law last year is estimated to cut Medicaid by amounts ranging from $665 billion to nearly $1 trillion over the next decade — but starting after the midterm elections. But those are cuts to the projected growth of the program; Medicaid spending will still increase, but by far less than it would have without the legislation.

The cuts are estimated to result in 7.5 million people losing Medicaid coverage by 2034, according to the Center on Budget and Policy Priorities, a left-leaning think tank.

TrumpRx, the website that Mr. Trump touts as offering Americans the lowest drug prices in the world, was also at issue. The site connects consumers with pharmaceutical companies that, after negotiations with the Trump administration, have agreed to sell roughly 80 brand-name medications at discount prices comparable to those in Europe.

But those prices are vastly higher than the price of comparable generic drugs. Senator Elizabeth Warren, Democrat of Massachusetts, called them “scam discounts,” noting that a drug that sold for several hundred dollars on TrumpRx could be bought for $16 in generic form.

The hearings put a spotlight on a comment that Mr. Kennedy made during an interview two years ago with the motivational speaker 19Keys, who focuses on empowering Black men. Mr. Kennedy, then running for president, proposed weaning American children off psychiatric medications, including for A.D.H.D. and depression, by sending them to “wellness farms,” where they would be free of cellphones and other distractions.

“Every Black kid is now just standard put on Adderall, on S.S.R.I.s, benzos, which are known to induce violence, and those kids are going to have a chance to go somewhere and get re-parented, to live in a community where there’ll be no cellphones, no screens” Mr. Kennedy said on the show.

Black Democrats, including Representative Terri A. Sewell of Alabama and Senator Angela Alsobrooks of Maryland, upbraided Mr. Kennedy for the remarks. He insisted he had not made them, then said he did not remember making them, then edged toward an apology.

“If I said it, I apologize, but I have to see the transcript,” he told Ms. Alsobrooks, who brought a huge placard bearing the quote to Wednesday’s health committee hearing.

The hearings came at a time of great flux for the secretary’s department. Last week, as Mr. Kennedy was in the middle of testifying in the House, Mr. Trump announced a four-person team to lead the Centers for Disease Control and Prevention. He nominated Dr. Erica Schwartz, whose supportive views on vaccines diverge sharply from Mr. Kennedy’s, to lead the agency, prompting questions about how much latitude the secretary would give her.

Mr. Kennedy told lawmakers he supported the nomination, but he refused to commit to accepting all of Dr. Schwartz’s decisions on vaccines. “I’m not going to make that kind of commitment,” he said on Tuesday.

When Wednesday’s hearing was over, Mr. Cassidy offered an oblique assessment of the secretary’s performance. “Things were illuminating,” he said.

President Trump’s selection of Dr. Casey Means, a Stanford-educated wellness specialist and book author, as his next surgeon general provoked a vigorous debate on Thursday over whether someone who is not a practicing physician should serve as the nation’s top doctor.

Laura Loomer, the far-right activist who holds so much sway with Mr. Trump that more than a half-dozen national security officials were fired on her advice, emerged as a vocal critic. So did Nicole Shanahan, Health Secretary Robert F. Kennedy Jr.’s former running mate, who called the choice “very strange.”

Dr. Means, a close ally of Mr. Kennedy’s, trained as a surgeon in otolaryngology — ear, nose and throat medicine — but left her surgical residency after four years to practice “functional medicine,” which focuses on the root causes of disease. She has said she was disillusioned with the medical establishment, and had concluded it was failing patients.

Ms. Loomer ridiculed Dr. Means on social media Thursday, calling her a “total crack pot” who “USES SHROOMS AS ‘PLANT MEDICINE’ AND TALKS TO TREES!” and “DOESN’T EVEN HAVE AN ACTIVE MEDICAL LICENSE.” As evidence, Ms. Loomer posted excerpts of Dr. Means’s weekly newsletter, in which Dr. Means muses on recipes, product recommendations and other topics, including “mindset shifts and habits.”

Mr. Kennedy pushed back hard with a lengthy post on X, calling the criticism “absurd,” while Mr. Trump told reporters that he did not know Dr. Means, but picked her because “Bobby thought she was fantastic.”

Dr. Means’s brother, Calley Means, a White House adviser on health issues and former food industry lobbyist, defended his sister in an interview.

“Casey has inspired millions of Americans and is a threat to the status quo because she left the medical system, not in spite of it,” Mr. Means said.

He added that the family had been shocked when she left her residency, “but she had a clear moral insight that her patients were not getting better.”

Under federal law, the surgeon general oversees the Commissioned Corps of the U.S. Health Service, the uniformed service that works on the front lines of public health.

There are just two requirements for the job: the nominee must be a member of the Corps (usually the president simply appoints a candidate before he or she takes the job) and must have “specialized training or significant experience in public health programs.”

Dr. David A. Kessler, a former head of the Food and Drug Administration who also served as dean of the medical schools at Yale and the University of California, San Francisco, said in an interview that while there may be legitimate reasons to criticize Dr. Means, not having a current medical license was not among them.

The main question, Dr. Kessler said, is whether a surgeon general is “well-trained” in medicine. If Dr. Means finished four years of residency, he said, “she is very well-trained.”

Major medical groups were largely silent on the appointment. Neither the American Medical Association nor the American Public Health Association issued statements. But Arthur L. Caplan, a prominent medical ethicist at New York University, called the appointment “irresponsible.”

“Appointing Casey Means, a non-practicing doctor who has spent years peddling unproven ‘health interventions,’ means a surgeon general that will put a fringe practitioner of unproven functional medicine in charge of educating the American people about their health and disease challenges,” Dr. Caplan wrote in an email.

Noting that Mr. Kennedy has called for placebo-controlled trials of vaccines, Dr. Caplan said the health secretary should apply the same scientific rigor to the type of functional and alternative remedies Dr. Means favors. “Without data it is akin to having her run Newark airport without radar or radio,” he wrote.

The Means siblings are both media-savvy wellness entrepreneurs. Calley Means is the founder of Truemed, a startup that enables tax-free spending on supplements, exercise and healthy food. Casey Means is the founder of Levels, a company that offers subscribers wearable glucose monitors to track their health.

Her embrace of holistic therapies has drawn some eye rolls in the press. Rolling Stone called her a “woo-woo wellness influencer.”

Dr. Means rose to prominence last year after she and her brother appeared on Tucker Carlson’s show to promote their diet and self-help book, “Good Energy,” which argues that metabolic dysfunction is at the root of a chronic disease epidemic.

Mr. Kennedy said on X that Dr. Means’s ability to “inspire Americans to rethink our health care system” was “an existential threat to the status quo interests, which profit from sickness.” In an interview with Fox News, he said she had “galvanized” his “Make America Healthy Again” movement.

Like Mr. Kennedy, Dr. Means has repeatedly said that America is in the midst of a chronic disease crisis. She has pointed to rising rates of infertility, obesity, diabetes, depression and other conditions as proof. Also like Mr. Kennedy, she has suggested that environmental toxins and the food system are to blame.

Mr. Trump’s appointment of Dr. Means came as a surprise. He announced it on Wednesday after withdrawing the nomination of his previous choice, Dr. Janette Nesheiwat, who was to appear before the Senate health committee on Thursday.

Dr. Nesheiwat, an urgent care physician and former Fox News commentator, is the sister-in-law of Michael Waltz, who served as Mr. Trump’s national security adviser until last week. She had faced criticism that she was less than forthcoming about her credentials; Ms. Loomer complained that Dr. Nesheiwat was not “ideologically aligned” with the president.

The surgeon general has no real authority to set policy; the power of the job is in the platform and in the surgeon general’s reports. The landmark 1964 report on tobacco led to warning labels on cigarette packages. Dr. C. Everett Koop, one of the nation’s best-known surgeon generals, used the office to advocate for patients with AIDS at a time when his fellow Republicans were ignoring the disease.

Dr. Vivek Murthy, who served as surgeon general in the Obama and Biden administrations, spoke out about loneliness and mental health.

Dr. David Perlmutter, an ally of Dr. Means’s whose work focuses on the intersection of nutrition and neurological disorders, said the most important quality for any surgeon general is the ability to communicate science to the public.

Dr. Means, he said, “excels at that.”

During his Senate confirmation hearings to be health secretary, Robert F. Kennedy Jr. presented himself as a supporter of vaccines. But in office, he and the agencies he leads have taken far-reaching, sometimes subtle steps to undermine confidence in vaccine efficacy and safety.

The National Institutes of Health halted funding for researchers who study vaccine hesitancy and hoped to find ways to overcome it. It also canceled programs intended to discover new vaccines to prevent future pandemics.

The Centers for Disease Control and Prevention shelved an advertising campaign for the flu shot. Mr. Kennedy has said inaccurately that the scientists who advise the C.D.C. on vaccines have “severe, severe conflicts of interest” in promoting the products and cannot be trusted.

The Health and Human Services Department cut billions of dollars to state health agencies, including funds needed to modernize state programs for childhood immunization. Mr. Kennedy said in a televised interview on Wednesday that he was unaware of this widely reported development.

The Food and Drug Administration canceled an open meeting on flu vaccines with scientific advisers, later holding it behind closed doors. A top official paused the agency’s review of Novavax’s Covid vaccine. In a televised interview last week, Mr. Kennedy said falsely that similarly created vaccines don’t work against respiratory viruses.

Some scientists said they saw a pattern: an effort to erode support for routine vaccination, and for the scientists who have long held it up as a public health goal.

“This is a simultaneous process of increasing the likelihood that you will hear his voice and decreasing the likelihood that you’ll hear other voices,” Kathleen Hall Jamieson, director of the Annenberg Public Policy Center, said of Mr. Kennedy.

He is “decertifying other voices of authority,” she said.

H.H.S. disagreed that Mr. Kennedy was working against vaccines.

“Secretary Kennedy is not anti-vaccine; he is pro-safety,” Andrew Nixon, a department spokesman, said in a statement. “His focus has always been on ensuring that vaccines are rigorously tested for efficacy and safety.”

The statement continued, “We are taking action so that Americans get the transparency they deserve and can make informed decisions about their health.”

After attending the funeral of an unvaccinated child who died of measles in West Texas on Sunday, Mr. Kennedy endorsed the measles vaccine on X as “the most effective way to prevent the spread of measles.”

But he has also described vaccination as a personal choice with poorly understood risks and suggested that miracle treatments were readily available. On Sunday, he praised two local doctors on social media who have promoted dubious, potentially harmful, treatments for measles.

Even as cases of measles in the United States have surged past 600 in 22 jurisdictions, Mr. Kennedy has claimed in a recent interview that the measles vaccine causes deaths every year (untrue); that it causes encephalitis, blindness and “all the illnesses that measles itself causes” (untrue); and that the vaccine’s effect wanes so dramatically that older adults are “essentially unvaccinated” (untrue).

According to an email obtained by The New York Times, H.H.S. intends to revise its web pages to include statements like “The decision to vaccinate is a personal one” and “People should also be informed about the potential adverse events associated with vaccines.” (Vaccines are already administered only after patients provide informed consent, as required by law.)

Tensions with mainstream experts came into sharp focus last week, when Dr. Peter Marks, the top vaccine regulator, resigned under pressure from the F.D.A.

“It has become clear that truth and transparency are not desired by the secretary, but rather he wishes subservient confirmation of his misinformation and lies,” Dr. Marks said in his resignation letter.

Mr. Kennedy’s position on vaccines has raised alarm for decades. But it has become particularly notable now, against a backdrop of rising skepticism of vaccines and worsening outbreaks of measles and bird flu, experts said.

The M.M.R. vaccine — a combination product to prevent measles, mumps and rubella that has been available since 1971 — has long been a target of anti-vaccine campaigns because of the disproved theory that it can cause autism. Mr. Kennedy has said that he would like to revisit the issue, in part to assuage parents’ fears that the vaccines are unsafe.

But he has hired David Geier to re-examine the data. Senator Bill Cassidy, Republican of Louisiana, a doctor and the chairman of the Senate Health Committee, has sharply criticized the decision to spend tax dollars testing a discredited hypothesis even as the administration is cutting billions for other research.

“If we’re pissing away money over here,” he said last month, “that’s less money that we have to actually go after the true reason.”

The refusal to accept scientific consensus is “disturbing, because then we get into very strange territory where it’s somebody’s hunch that this does or doesn’t happen, or does or doesn’t work,” said Stephen Jameson, president of the American Association of Immunologists.

In interviews, Mr. Kennedy has downplayed risks of measles and emphasized what he sees as the benefits of infection.

“Everybody got measles, and measles gave you protected lifetime protection against measles infection — the vaccine doesn’t do that,” he said in an interview on Fox News.

Two doses of the M.M.R. vaccine do provide decades-long immunity. And while immunity from the infection may last a lifetime, “people also suffer the consequences of that natural infection,” Dr. Jameson said.

One consequence was discovered just a few years ago: A measles infection can destroy the immune system’s memory of other invading pathogens, leaving the body vulnerable to them again.

Measles kills roughly 1 in every 1,000 infected people, and 11 percent of those infected this year have been hospitalized, many of them children under 5, according to the C.D.C. Two girls, ages 6 and 8, died in West Texas.

By contrast, side effects after vaccination are uncommon. But Mr. Kennedy has suggested that people should apprise themselves of the risks before opting for the shot.

The phrasing implies that “if you are more fully informed, you might make a different decision,” said Dr. Jamieson, of the Annenberg center.

Doctors have long expected health secretaries and the C.D.C. to urge widespread vaccination unequivocally amid an outbreak, and in the past they have.

But Mr. Kennedy has spoken enthusiastically about cod liver oil, a steroid and an antibiotic that are not standard therapies. Some of those treatments may be making children more sick.

“The messaging I’m seeing is focused on potential treatments for measles,” said Dr. Sean O’Leary, chair of the infectious disease committee for the American Academy of Pediatrics.

Closed Doors

At his confirmation hearing, Mr. Kennedy promised that he would not change the C.D.C.’s childhood vaccination schedule. About two weeks later, he announced a new commission that would scrutinize it.

The schedule is based on recommendations from the Advisory Committee on Immunization Practices, a panel of medical experts who review safety and effectiveness data, potential interactions with other drugs and the ideal timing to maximize protection.

At his confirmation hearing, Mr. Kennedy claimed that 97 percent of A.C.I.P. members had financial conflicts of interest. He has long held, without evidence, that federal regulators are compromised and are hiding information about the risks of vaccines.

“It’s frankly false,” said Dr. O’Leary, who serves as a liaison to the committee from the pediatric academy.

Mr. Kennedy’s statistic came from a 2009 report that found that 97 percent of disclosure forms had errors, such as missing dates or information in the wrong section.

In fact, A.C.I.P. members are carefully screened for major conflicts of interest, and they cannot hold stocks or serve on advisory boards or speaker bureaus affiliated with vaccine manufacturers.

On the rare occasion that members have indirect conflicts of interest — for example, if an institution at which they work receives money from a drug manufacturer — they disclose the conflict and recuse themselves from related votes.

The committee’s votes were public and often heavily debated.

“When I was C.D.C. director, people flew in from Korea and all over the world to observe the A.C.I.P. meetings, because they were a model of transparency,” said Dr. Thomas R. Frieden, who led the agency from 2009 to 2017.

Mr. Kennedy has repeatedly promised greater transparency and accountability, but he has proposed ending public comment on health policies.

His department canceled a meeting of the A.C.I.P. in February at which members were set to discuss vaccines for meningitis and flu, rescheduling it for April.

The department also canceled a meeting to discuss the seasonal flu vaccine. Officials met later without the agency’s scientific advisers.

“After all that conversation about how they want to be transparent, one of the first things he does is take things behind closed doors and diminish the amount of public input we’re getting,” said Dr. Georges Benjamin, executive director of the American Public Health Association.

At his confirmation hearing, Mr. Kennedy repeated a fringe theory that Black Americans should not receive the same vaccines as others because they “have a much stronger reaction.”

Senator Angela Alsobrooks, Democrat of Maryland, who is Black, admonished him for his “dangerous” opinion: “Your voice would be a voice that parents would listen to.”

Two weeks later, at a clinic for teenage mothers in Denver, a 19-year-old woman refused all vaccines for herself and her 1-year-old son — including the measles and chickenpox shots he was supposed to have that day.

She told the pediatrician, Dr. Hana Smith, who described the incident, that she had read online that vaccines were bad for people with more melanin in their skin.

There are reams of evidence to the contrary. Still, it quickly became clear to Dr. Smith that nothing was going to change her patient’s mind.

“No matter how much information I can give to the contrary on it, the damage is already done,” Dr. Smith said.

Misinformation is particularly difficult to counter, Dr. Smith said, “when it’s someone that has a leadership position, especially within the health care system.”