Robert F. Kennedy Jr. spent the first day of his back-to-back confirmation hearings deftly avoiding questions about his views on vaccines. On the second day, when a prominent Republican senator insisted there was no link between vaccines and autism, Mr. Kennedy shot back that a new study “showed the opposite.”

“I just want to follow the science,” Mr. Kennedy declared.

Following the science has been a familiar refrain for Mr. Kennedy, whose confirmation as health secretary appears all but assured in a vote expected Thursday. But the exchange in the Senate raises questions about just what type of science Mr. Kennedy is consulting. It foreshadows how, if confirmed, Mr. Kennedy could continue to sow doubts about vaccines.

Academics have pounced on the study that Mr. Kennedy cited during the hearing, shredding it as methodologically faulty and biased. The study emanated from a network of vaccine skeptics who share some of Mr. Kennedy’s views — an ecosystem that includes the author of the study, the editor of the journal that published it and the advocacy group that financed it.

“We authors were delighted and honored that R.F.K. Jr. referred to our work in his confirmation hearing,” the study’s lead author, Anthony Mawson, said in an email. A spokeswoman for Mr. Kennedy did not respond to a request for comment.

Dr. Mawson, an epidemiologist, said he first met Mr. Kennedy at an autism conference in 2017. Mr. Kennedy cites Dr. Mawson’s research 33 times in his 2023 book, “Vax-Unvax: Let the Science Speak.”

His study was rejected “without explanation” by several mainstream medical journals, Dr. Mawson said. So he turned for advice to Andrew Wakefield, the author of the 1998 study, now retracted, that sparked the initial furor over vaccines and autism. Mr. Wakefield encouraged him to submit the study to a new journal called Science, Public Health Policy and the Law.

That publication is led by some notable vaccine critics, including three who headlined a Washington rally in 2022 with Mr. Kennedy to protest Covid vaccine mandates.

As the nation’s health secretary, Mr. Kennedy “would have wide powers to advance his favored research studies, publications, or scientific data,” according to Lawrence O. Gostin, a public health law expert at Georgetown University. Mr. Kennedy’s critics fear that the public will have neither the time nor the training to sort through a war that seems to pit one study against another, and that the result will be a rapid decline in confidence in vaccines.

“The Mawson paper epitomizes Kennedy’s consistent inability to distinguish junk science from reliable information,” said Dr. John P. Moore, professor of microbiology and immunology at Weill Cornell Medical College, who said that study and some of the others Mr. Kennedy has cited in the past are published by “fringe journals.”

Mr. Kennedy has said that he is not anti-vaccine, but rather in favor of vaccine safety.

“I support the measles vaccine. I support the polio vaccine,” Mr. Kennedy said on the first day of his confirmation hearings. “I will do nothing as H.H.S. secretary that makes it difficult or discourages people from taking it.”

Mr. Kennedy’s insistence that more research is necessary when it comes to vaccine safety has drawn support from some Republicans, who say they welcome his skepticism.

“I don’t understand why my colleagues all of sudden say we can’t question science,” Senator Markwayne Mullin, Republican of Oklahoma, said during one of Mr. Kennedy’s hearings. He added, “When you start looking at the rise of autism, why wouldn’t we be looking at everything?”

But Michael T. Osterholm, an epidemiologist at the University of Minnesota who has advised administrations of both parties, said Mr. Kennedy’s demands for additional data go too far when they concern vaccines and autism. Mainstream scientists say the issue is settled.

“That’s the equivalent of me saying until Newton comes back and shows me that apple falling from the tree, I do not believe gravity exists,” Dr. Osterholm said.

Doctors who have examined the way Mr. Kennedy uses scientific research say he also has a tendency to cherry-pick particular findings from prominent researchers, as he did during a podcast in 2022.

During that appearance, he cited a study published in the journal Pediatrics in 2000 to suggest that improvements in sanitation and hygiene — and not vaccines — fueled a drop in deaths from infectious diseases during the first half of the 20th century. That is true. But Mr. Kennedy failed to note that the study also reported that vaccines introduced in the second half of the 20th century had “virtually eliminated” deaths from diseases including polio and measles.

During one of his confirmation hearings, Mr. Kennedy cited work by a well-known vaccine scientist, Dr. Gregory Poland, to suggest Black people should follow a different vaccine schedule because they needed fewer antigens, the vaccine components that provoke an immune response.

Dr. Poland did not respond to requests for comment. But he told National Public Radio that his work did not support Mr. Kennedy’s assertion.

Mr. Kennedy and Dr. Mawson have long aired similar concerns about vaccines.

In an appearance before the Mississippi legislature in 2009, Dr. Mawson called for more vaccine safety research and “a more flexible approach to vaccination requirements for school attendance.” In a 2011 lawsuit, Dr. Mawson said the testimony had cost him his job as an epidemiologist at the University of Mississippi Medical Center.

In 2017, Dr. Mawson published a pilot study comparing vaccinated to unvaccinated children.

The study relied on a survey of parents who home-schooled their children and found higher rates of autism among vaccinated children, compared with those who had not been vaccinated. The study was funded in part by Generation Rescue, a nonprofit associated with Jenny McCarthy, a television personality who has promoted claims of a link between vaccines and autism.

Dr. Mawson by that time had established the Chalfont Research Institute, a charity that operates out of his home in Jackson, Miss. The institute reported revenue of just $57 in 2021, the most recent figures available.

In 2019, it received charitable contributions of $160,000, tax records show. The bulk of that money, $150,000, came from the National Vaccine Information Center, a group whose mission includes supporting research on “vaccine-associated deaths, injuries and chronic illness.”

Like Mr. Kennedy, the group’s president and co-founder, Barbara Loe Fisher, has long called for research comparing “total health outcomes” including the risk of autism, in vaccinated and unvaccinated children. When Dr. Mawson approached her group with a proposal, she said, the center reviewed his pilot study of 2017, approved his plan and provided $150,000 in funding.

That money paid for the paper Mr. Kennedy cited at the hearing, during an exchange with Senator Bill Cassidy, Republican of Louisiana and a doctor.

The journal that published the study, Science, Public Health Policy and the Law, advertises itself as peer-reviewed, meaning its research is evaluated by anonymous independent experts before publication. Dr. Mawson said his paper had undergone review by two such experts.

Some people associated with the journal are also associated with Mr. Kennedy.

James Lyons-Weiler, the journal’s editor in chief, described himself as a longtime ally of Mr. Kennedy’s in a yearslong “fight across 20 states” for vaccine exemptions.

“Honored to call him my friend,” he wrote on social media last year.

The journal’s editorial board includes the chief executive and the chief scientific officer of Children’s Health Defense, the nonprofit that Mr. Kennedy led until he began his presidential campaign in 2023.

The board also includes members who sell products or services for people who are concerned about vaccines. One of its editorial board members offers $2,350 telehealth appointments for “post-vaccine syndrome.” Another sells $90 “spike detox” supplements marketed for “vaccine injury syndrome” that is meant to get “you back to that pre-Covid feeling.”

The study by Dr. Mawson that Mr. Kennedy cited at the hearing focused on about 47,000 children enrolled in Florida Medicaid from 1999 to 2011 and looked at billing data to determine their vaccination status.

The study found very few billing records for unvaccinated children with autism — eight who were born prematurely and 54 overall. It concluded that vaccination was significantly associated with higher rates of neurodevelopmental disorders, including autism, particularly in infants who were born prematurely.

By contrast, large-scale studies in respected medical journals, including an analysis of five studies involving more than 1.2 million children, have found no association between vaccines and autism.

But even as Dr. Mawson’s research took shape, problems emerged. The paper notes that researchers lost access to the database they used to perform the study. Dr. Alex Morozov, an expert on clinical trial design who met with Dr. Mawson to discuss the study, said he viewed that as a red flag.

Dr. Morozov also said the study had a “fundamental flaw”: It failed to account for the possibility that vaccinated children might have more encounters with the medical system than unvaccinated children, whose illnesses would not be captured by billing data.

The study also failed to account for factors like family history of autism, the child’s gender (boys are diagnosed with higher rates of autism than girls) or the possibility that children might have been vaccinated outside the Florida Medicaid system, said Bertha Hidalgo, an associate professor of epidemiology at the University of Alabama at Birmingham.

Dr. Mawson strongly defended the work, noting that the study “carefully documents both its strengths and limitations,” but contending that critics focused only on the limitations. “Nevertheless,” he said, “further research is needed to replicate the findings and to unravel the mechanisms involved.”

At the Senate hearing, Mr. Cassidy pressed Mr. Kennedy to accept that the vaccines and autism debate was settled. He reminded Mr. Kennedy that he had been shown the study of 1.2 million children that found no link between the two.

“I’m a doc, trying to understand,” Mr. Cassidy said, adding, “Convince me that you will become the public health advocate, but not just churn old information so that there’s never a conclusion.”

To that, Mr. Kennedy replied, “I’m going to be an advocate for strong science. You show me those scientific studies, and you and I can meet about it. And there are other studies as well. I’d love to show those to you.”