Health Secretary Robert F. Kennedy Jr. has said little publicly about vaccines in recent months, at the behest of a White House worried that his unpopular stance will hurt Republicans in November’s midterm elections. But he has not abandoned his quest for evidence that they are unsafe.

Working behind the scenes, Mr. Kennedy is spearheading an intense push, across health agencies under his purview, for government scientists and federal data contractors to examine his long-held theory that vaccines are helping to fuel an epidemic of chronic disease, according to multiple people familiar with the effort.

They said the wide-ranging inquiry is a top priority for Mr. Kennedy, who sees vaccines as a “potential culprit” in various neurological and autoimmune disorders, including asthma and allergies. It resurrects research into a number of ideas Mr. Kennedy has espoused, including whether vaccines are linked to autism and whether thimerosal, a preservative that has largely been removed from vaccines in the United States but remains in some flu shots, is dangerous.

The effort is being led by Martin Kulldorff, a biostatistician and vaccine safety expert who rose in prominence during the pandemic as a critic of Covid restrictions and vaccine mandates, and is now the health department’s chief science and data officer.

Career scientists at the Food and Drug Administration and the Centers for Disease Control and Prevention are conducting the research alongside contractors who provide statistical expertise and access to millions of patient medical records. The initiative was described to The New York Times by six people who are close to it, all of whom insisted on anonymity because it is not public.

The work is raising alarms among some vaccine scholars and critics of Mr. Kennedy, who have long accused the secretary of cherry-picking data and misinterpreting studies to claim that vaccines are unsafe and to limit their use. They fear Mr. Kennedy will use the findings to further erode confidence in vaccines, which the World Health Organization estimates saved 154 million lives over the past half-century.

Mr. Kennedy, who came into office saying he would do nothing to discourage people from getting vaccinated, has already taken steps to scale back the number of vaccines children receive. Public health experts complain that by spending money on issues that have already been thoroughly studied, he is taking funds away from research that might answer the very questions he is asking, including what causes autism.

“It just demonstrates that no matter what the general tone is about vaccines, whether we talk about them or not, the secretary is going to continue to try and look at the data and analyze it in a way that will help support the conclusions that he’s already made,” said Dr. Daniel Jernigan, who oversaw vaccine safety at the C.D.C. until he resigned in August. “And that, to me, is a real problem.”

Andrew Nixon, a spokesman for Mr. Kennedy, said in a statement that the effort reflected President Trump’s dedication to advancing “gold-standard vaccine research” that will enable policymakers to “better understand vaccine safety and efficacy and to assess how vaccine exposure, timing and patterns affect health across the life span.”

Mr. Nixon said the work would “inform vaccine recommendations, address critical gaps identified by scientific and medical organizations, including the Institute of Medicine, and strengthen public trust in public health.”

He said the initiative also involved the National Institutes of Health and universities. It remains unclear what the effort will cost and whether it is supplanting other routine government vaccine surveillance.

A former plaintiff’s lawyer, Mr. Kennedy has long said that he wants to build a body of scientific evidence on the harms of vaccines and environmental exposures, which he believes are behind an epidemic of chronic disease. That evidence, he has said, will lay the groundwork for legal action.

“That’s how you really change policy,” Mr. Kennedy said in a podcast as a presidential candidate in 2024. He added, “I’m going to provide that enough science, sufficient science, on each one of these exposures and each one of these injuries, to show who’s causing what and hold them responsible in court.”

During a daylong meeting on the new vaccine research initiative in late February, officials from the Health Department and the C.D.C. gathered to discuss specific studies and methods, including a look at the overall effect of the childhood vaccine schedule. Representatives from major health systems such as Kaiser Permanente were also at the table, given their role in allowing the C.D.C. access to vast troves of data through its Vaccine Safety Datalink system.

As part of the new effort, Mr. Kennedy has tasked some government scientists with studying the health status of vaccinated children compared with those who were not vaccinated. Mr. Kennedy coauthored a book, “Vax-Unvax: Let the Science Speak,” calling for such studies, which he believes will prove harm from vaccines.

Researchers say that such comparison studies would be riddled with pitfalls. Vaccinated children are more likely to receive medical care than those who are unvaccinated, and are thus more likely to receive additional medical diagnoses that could be wrongly attributed to vaccines.

Mr. Kennedy is also asking for the group to undertake new studies looking at the link between vaccines and autism.

The project is also looking at the question of harm from thimerosal, a mercury-based vaccine preservative, according to people close to the effort. The preservative has been thoroughly studied and found to be unrelated to autism, but Mr. Kennedy has remained concerned about it, and has rescinded federal recommendations for flu vaccines that contain thimerosal.

Through the C.D.C. alone, the cost of the project is estimated at $40 million to $50 million, according to a person familiar with the matter.

The project is being overseen by Mr. Kennedy and Stefanie Spear, his closest adviser. Mr. Kennedy’s new senior counselor for public health, Dr. Sara Brenner, a veteran of the F.D.A. who has voiced skepticism of vaccines, is expected to propel the studies forward in her new role, according to people familiar with the plan.

The new vaccine initiative is not the first time the secretary has waged a behind-the-scenes effort to study vaccine safety. Last year, Mr. Kennedy faced significant pushback within federal agencies and from Congress when he deployed David Geier, whose vaccine research is considered deeply flawed, to dig into vaccine safety data to explore some of the secretary’s longstanding concerns.

Mr. Kennedy’s team put pressure on C.D.C. officials, including Dr. Jernigan, who delayed Mr. Geier. When Mr. Kennedy ousted Susan Monarez, the agency’s director, Dr. Jernigan and other C.D.C. leaders quit.

Within the C.D.C. and F.D.A., scientists have registered some relief that Dr. Kulldorff, a pioneer in methods to examine vaccine safety, is leading the new inquiry. He worked on research that was groundbreaking in 2009 to monitor the safety of the H1N1 flu vaccine as it was being rolled out. The team he worked with found a slightly elevated rate of Guillain-Barré syndrome, an autoimmune condition associated with some vaccines.

“Martin had been known for decades as a top-notch vaccine safety scientist,” said Daniel Salmon, a Johns Hopkins University vaccine researcher who worked with Dr. Kulldorff on a vaccine data system that predated one the F.D.A. now uses.

Some scientists who worked with Dr. Kulldorff in the past, though, wonder if the evenhanded biostatistician they once knew changed during the pandemic. They point to a federal document, coauthored by Dr. Kulldorff, justifying sharp limitations on vaccines recommended to children in the United States, saying it left out reams of studies supporting flu and hepatitis B vaccines for infants and children.

In 2024, Dr. Kulldorff joined Mr. Kennedy in litigation against Merck, the makers of Gardasil, a vaccine for the human papilloma virus, earning $400 per hour as an expert witness, court records show. Merck, the vaccine’s maker, challenged Dr. Kulldorff’s standing as an expert based on his prior research finding that the vaccine was safe.

Dr. Kulldorff did not respond to a request for comment, and the health department did not respond to a request to make him available. Mr. Kennedy and Ms. Spear also did not respond to requests for comment.

The C.D.C. and the F.D.A. already devote considerable effort to investigating vaccine safety, using a number of databases and research methods. But Mr. Kennedy’s fellow vaccine critics, including Retsef Levi, a mathematician at the Massachusetts Institute of Technology who serves on Mr. Kennedy’s handpicked a panel of C.D.C. vaccine advisers, find fault with the current studies.

“Many of them have serious methodological flaws,” Dr. Levi said.

Mr. Kennedy began raising questions about vaccines’ safety about 20 years ago, and became a champion for mothers of children with autism who blamed the condition on vaccines. People familiar with his thinking say he still feels deeply committed to those women, and cannot reconcile their often heartbreaking stories with the vast body of research that discounts a link.

For parents who believe vaccines have harmed their children, Mr. Kennedy is fulfilling a major promise. Katie Wright, whose 24-year-old son has autism and got to know Mr. Kennedy through her advocacy for parents who question the safety of vaccines, said more research is necessary to restore trust in childhood immunization.

“There’s been tremendous pushback; they say, ‘Well, the research has been done.’ ” Ms. Wright said. “Well, you know what? A lot of families are concerned. I don’t understand the fear of delving deeper into safety research.”

As health secretary, Mr. Kennedy has demonstrated an unorthodox view of what makes for reliable findings about vaccines. He dismissed a major vaccine study of 1.2 million Danish children over 24 years as “a deceitful propaganda stunt,” for failing to highlight a subset of about 50 children who were more likely to have gotten Asperger’s syndrome, a diagnosis previously applied to high-functioning people with autism, after getting vaccines.

In the language of vaccine science, such findings are considered a signal to be examined in more depth. Dr. Kathryn Edwards, a Vanderbilt University expert in vaccinology, said she was concerned that selective attention to such signals could be “used to further erode the confidence that people have in vaccines.”

Mr. Kennedy has also made hasty changes to vaccine policy, often with minimal scientific justification for decision making. Among those pivots was an overhaul in January of vaccine recommendations, reducing the number of immunizations for American children to 10 from 17.

Though the plan was held up in court, Dr. Edwards said it portends a scenario where the findings of the current effort get a big splash in the media or drive new policies before scientists can understand the reasoning.

“What they’ve done is also worrisome,” she said, “because there have been so many things that haven’t been open and transparent.”