As the Trump administration clamped down on the country’s medical research funding apparatus in recent months, scientists and administrators at the National Institutes of Health often privately wondered how much autonomy the agency’s director, Dr. Jay Bhattacharya, had.

After all, the Department of Government Efficiency, Elon Musk’s signature cost-cutting project, helped drive decisions to cancel or delay research grants. Other projects fell victim to President Trump’s face-off with universities over antisemitism. But given an opportunity before a Senate panel on Tuesday to dispel suspicions about who wields influence at the N.I.H., Dr. Bhattacharya did little to claim ownership of perhaps the rockiest period in the agency’s many decades of funding research institutions.

Decisions to freeze grant payments to Northwestern University “happened before I got into office,” Dr. Bhattacharya told the panel, members of the Senate Appropriations Committee.

He repeatedly said a proposal to shrink the N.I.H. budget by $18 billion — nearly 40 percent — was “a collaboration between Congress and the administration” and declined to talk in detail about how the cuts would affect the agency.

And pressed on an effort to curtail funding to universities for research overhead expenses — a cost-cutting move that is baked into the administration’s 2026 budget proposal — Dr. Bhattacharya said, “I don’t want to get into that,” citing ongoing litigation.

Several Democrats on the committee said they were confused about who was pulling the strings at the agency.

“I want to know, who is withholding this funding?” demanded Senator Tammy Baldwin of Wisconsin, a Democrat, citing evidence that the N.I.H. had distributed billions of dollars less in grants so far this year than in the same period last year. “Is it you? Is it DOGE? Is it O.M.B.?” she added, referring to the Office of Management and Budget. “Who is making those decisions?”

Dr. Bhattacharya responded, “There’s a range of decisions, I think, that led to some of those pauses of grants.” He said, for example, that it had been his call to move away from what he called “politicized science,” a term he has used in the past to describe research related to diversity and equity issues. But he said that restrictions on research funding at Harvard and other leading institutions had been “joint with the administration.”

Senator Dick Durbin of Illinois, another Democrat, reacted sharply after Dr. Bhattacharya denied responsibility for the administration’s freezing research payments to Northwestern.

An email from an N.I.H. official in mid-April, weeks after Dr. Bhattacharya’s confirmation, directed employees not to issue grant awards to Northwestern and several other universities and not to tell the institutions why their funding had been frozen.

“The buck stops in your office,” Mr. Durbin told Dr. Bhattacharya. “Don’t blame another person.”

The Trump administration’s effort to significantly shrink the agency’s spending next year drew criticism from senators of both parties, including Senator Susan Collins of Maine, a Republican.

The proposed reduction “is so disturbing,” she told Dr. Bhattacharya. “It would delay or stop effective treatments and cures from being developed for diseases like Alzheimer’s, cancer, Type 1 diabetes.” The plans, she said, put the United States at risk of “falling behind China.”

Dr. Bhattacharya said that the N.I.H. was committed to research on Alzheimer’s and other diseases and that he would work with lawmakers to address “the health needs of all Americans.”

The director did open the door to an agreement between the Trump administration and leading universities that would unfreeze their medical research funding, although he offered no details about the prospects for such an agreement or what it would take to arrive at one. “I’m very hopeful that a resolution can be made with the universities where those grants have been paused,” he said.

The N.I.H. in recent months has abruptly ended more than 1,300 grant awards and delayed funding for more than 1,000 other projects. On Monday, scores of N.I.H. employees signed their names to a letter saying those actions had been undertaken on the basis of ideological preferences and without scientific staff input, effectively censoring research on issues like health disparities, Covid, the health effects of climate change and sexual health.

Dr. Bhattacharya said on Tuesday that he had set up a process for scientists to appeal funding cuts. The agency, he said, would vet appeals within weeks.