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.