Under hostile questioning from senators of both parties, Dr. Jay Bhattacharya, President Trump’s nominee to lead the National Institutes of Health, said on Wednesday that he was “convinced” vaccines did not cause autism even as he urged more research on the question, which scientists say has long been settled.

The hearing became a battlefield for the Trump administration’s early actions on health, including Health Secretary Robert F. Kennedy Jr.’s reluctance to explicitly recommend vaccinations in the midst of a deadly measles outbreak in West Texas.

“I fully support children being vaccinated for diseases like measles,” Dr. Bhattacharya, a health economist and professor of medicine at Stanford University, told the Senate Health Committee. But to assuage skeptical parents, he also said scientists should conduct more research on autism and vaccines — a position that senators from both parties noted was at odds with extensive evidence showing no association between them.

If confirmed, Dr. Bhattacharya would lead the world’s largest funder of biomedical research, a sprawling agency with a $48 billion budget and 27 separate institutes and centers that has long been praised by lawmakers on both sides of the aisle.

Recently, though, the N.I.H. has been rocked by Trump administration moves that blocked key parts of its grant-making apparatus and resulted in the firing of roughly 1,200 employees. Together with other lapses and proposed changes in N.I.H. funding, the administration’s actions have rattled the biomedical research industry, which is responsible for driving pharmaceutical advancements and generating tens of billions of dollars in economic activity each year.

Hours before Wednesday’s hearing, the Department of Government Efficiency, the cost-cutting group led by Elon Musk, trumpeted the cancellation of N.I.H. grants.

Asked about blockages to N.I.H. funding during the hearing, Dr. Bhattacharya repeatedly dodged, saying only that he would ensure scientists had the resources they needed. He vowed to direct funding toward the causes of chronic disease — a priority of Mr. Kennedy’s — and to create a “culture of dissent” that encourages the challenging of prevailing views.

He also promised to scrutinize research findings that were not borne out by subsequent studies and fund the most innovative research, producing “big advances” rather than “small, incremental progress.”

But it was Dr. Bhattacharya’s resistance to weigh in on N.I.H. funding stoppages and his equivocal answers on vaccines that drew the ire of Democrats and some Republicans.

In one contentious exchange, Senator Bill Cassidy of Louisiana, the committee’s Republican chairman, lamented that Dr. Bhattacharya had stopped short of saying the question of whether vaccines cause autism had been resolved.

“It’s been exhaustively studied,” said Mr. Cassidy, a doctor and fierce supporter of vaccination. “The more we pretend like this is an issue, the more we will have children dying from vaccine-preventable diseases.”

Dr. Bhattacharya responded that more research was needed as long as American parents were concerned enough not to vaccinate their children. “My inclination is to give people good data,” he said.

To that, Mr. Cassidy suggested that there already was good data, and that “precious limited taxpayer dollars” could not be devoted to every last fringe theory.

“There’s people who disagree that the world is round,” he said. “People still think Elvis is alive.”

Dr. Bhattacharya would not say whether he supported the Trump administration’s changes to N.I.H. funding, telling senators he had nothing to do with them. That did not stop numerous Democrats and one Republican, Senator Susan Collins of Maine, from attacking the changes, including a proposal to cap overhead costs. A judge has temporarily blocked that proposal.

“To impose this arbitrary cap makes no sense at all,” Ms. Collins said. “This is against the law.”

Dr. Bhattacharya, who has a medical degree and is a professor of medicine but never practiced, burst into the spotlight in October 2020, when he co-wrote an anti-lockdown treatise, the Great Barrington Declaration. It argued for “focused protection” — a strategy to protect the elderly and vulnerable while letting the virus spread among younger, healthier people.

Many scientists countered that walling off at-risk populations from the rest of society was a pipe dream.

The nation’s medical leadership, including Dr. Francis S. Collins, who retired last week, and Dr. Anthony S. Fauci, then director of the National Institute of Allergy and Infectious Diseases, denounced the plan. Referring to Dr. Bhattacharya and his co-authors as “fringe epidemiologists,” Dr. Collins wrote in an email that “there needs to be a quick and devastating takedown of its premises.”

Dr. Bhattacharya told senators on Wednesday that he had been “subject to censorship by the actions of the Biden administration.” Past N.I.H. officials, he said, “oversaw a culture of cover-up, obfuscation and a lack of tolerance for ideas that differ from theirs.”

But Dr. Bhattacharya’s championing of “scientific dissent” has sometimes clashed with his own actions. Until resigning late last year, he sat on the board of Biosafety Now, a group that promoted prosecuting “those culpable for covering up” the cause of Covid. Supporters of the theory that Covid leaked from a lab have often used that designation to refer to scientists who took different views.

On Wednesday, Dr. Bhattacharya waded again into the question of a laboratory leak, and whether N.I.H.-funded research at a virology laboratory in China led to one.

There is no direct evidence of the coronavirus escaping from a lab. Much published scientific research points instead to the virus emerging at a market in Wuhan, China, where wild animals were being illegally sold.

But Dr. Bhattacharya said that N.I.H.-supported research “may have caused the pandemic.” (The C.I.A. also recently swung in favor of the lab leak theory, though there was no new intelligence behind its shift and the agency has produced no direct evidence.) And Dr. Bhattacharya cast doubt over the future of American research on dangerous viruses, saying that the N.I.H. should not be doing “any research that has the potential to cause a pandemic.”

There has long been spirited debate over what type of research constitutes such a risk, and whether limiting that research would reduce the likelihood of another pandemic or instead undercut preparations for one.

Several senators noted that Dr. Bhattacharya had in the past received N.I.H. funding for his work. Some of that work, researchers have noted, may very well have run afoul of the Trump administration’s recent crackdown on certain types of science. The administration has targeted research related to climate science, for example, as well as studies touching on diversity, equity and inclusion.

In one ongoing project, Dr. Bhattacharya and several collaborators proposed using data from the Mexican Health and Aging Study, a longitudinal study of older Mexicans, to look at how climate change and workplace environmental exposures were related to disparities in Alzheimer’s disease.