The National Institutes of Health will no longer allow American scientists to direct its funding to research partners overseas, casting doubt on the future of studies on subjects including malaria and childhood cancer.

Dr. Jay Bhattacharya, the new director of the N.I.H., announced the policy on Thursday, the same day Dr. Matthew J. Memoli, the principal deputy director, blasted these so-called subawards in an email obtained by The New York Times.

“If you can’t clearly justify why you are doing something overseas, as in it can’t possibly be done anywhere else and it benefits the American people,” Dr. Memoli wrote, “then the project should be closed down.”

The new restrictions, which will apply to domestic subawards as well in the future, come amid deep reductions in N.I.H. funding and the freezing of federal grants at many top universities, along with executive orders seeking to reshape the nation’s scientific agenda.

On Monday, President Trump signed an executive order restricting a type of experimentation that can make pathogens more dangerous to humans, and ending support for the so-called gain-of-function research in countries like China.

Researchers funded by N.I.H. grants have historically used subawards to facilitate international collaborations, which are essential for studying conditions like childhood cancer or illnesses like malaria and tuberculosis that are not prevalent in the United States.

The subawards are legal and financial agreements made between the grant recipients and their overseas partners. The practice is used throughout the federal government and is not unique to the N.I.H.

But it has come under fire in recent years because of lax reporting and tracking of funds. After a critical report by the Government Accountability Office in 2023, the N.I.H. put stricter monitoring requirements in place.

Advocates for scientific and medical research said that as science has become more complex, collaborative initiatives that draw participants and scientists from around the world have become more critical.

“Competitive science requires a team approach,” said Dr. E. Anders Kolb, chief executive of the Leukemia & Lymphoma Society. “There’s no one lab or institution or investigator that has all of the tools necessary to solve the very complex questions that we’re asking.”

Many of these studies require a large number of subjects. For example, as scientists are able to define types of childhood cancers more precisely, Dr. Kolb said, “you get into increasingly smaller and smaller subsets of disease.”

“So if you want to run a clinical trial of a new therapy that may benefit those children, it could take decades to complete a trial if you only enroll children in the U.S.,” he added. “When we collaborate with our international partners, we can finish these trials much more quickly and get the therapies to children as soon as possible.”

In announcing the new directive, Dr. Bhattacharya cited recent Government Accountability Office reports that have been critical of funding given to international universities and laboratories, as well as businesses.

The issues highlighted by the G.A.O. reports “can lead to a breakdown in trust and potentially the security of the U.S. biomedical research enterprise,” Dr. Bhattacharya added.

N.I.H. spending on these international groups is difficult to track, one of the faults noted by the G.A.O. The journal Nature, which first reported the new policy, estimated the total at approximately $500 million a year.

Dr. Monica Gandhi, a professor of medicine at the University of California, San Francisco, has N.I.H. funding to study H.I.V. prevention and treatment in Kenya and South Africa, work that will be affected by the new policy.

Researchers like her must provide detailed information about international subawards when they apply for their grants, she said, including justifications for using a foreign entity and for each aspect of the budget.

International partners must now provide access to their lab notebooks, data and other documentation at least once a year, Dr. Gandhi noted. All of the expenditures are tracked on a system called the Foreign Award and Component Tracking System, or FACTS, she said.

“It’s very rigorous, as it should be when you’re using taxpayer dollars,” Dr. Gandhi said.

“Every year when you put in your progress report, you account for every penny that was spent at the foreign site — where it went, how much to lab tests, how much was paid investigators, every aspect.”

It wasn’t immediately clear how the new policy would be implemented. The N.I.H. did not respond to requests for additional information.

The N.I.H. will not retroactively halt foreign subawards already in place “at this time” and will continue to make awards directly to international groups, the agency’s statement said.

But the new policy will forbid new competing awards and noncompeting awards to be reissued if they propose subawards to foreign institutions.

“If a project is no longer viable without the foreign subawards, N.I.H. will work with the recipient to negotiate a bilateral termination of the project,” the statement said.

The new policy appeared to be somewhat less draconian than the summation put forth by Dr. Memoli in his internal email, which threatened immediate action to shut down or pause international sites.

“Subawards to foreign sites can’t continue,” he wrote. “This has been horribly mismanaged for years and it has been completely irresponsible. We must take immediate action. If a study has a foreign site we need to start closing it down or finding a different way to fund it that can be tracked properly.”

G.A.O. reports that had criticized various federal departments for lax reporting had called for improving oversight. But the office did not recommend terminating such funding altogether.

In 2023, a G.A.O. report reviewed $2 million in direct awards and subawards, most of it from the N.I.H., given to three Chinese research institutions, including the Wuhan Institute of Virology, between 2014 and 2021.

The virology institute received subawards from the University of California, Irvine, and from the nonprofit group EcoHealth Alliance. The alliance’s work with Chinese scientists led former President Joseph R. Biden Jr. to suspend its funding last year. The Trump administration recently changed the government portal for Covid information with a website suggesting that the new virus originated in a lab in Wuhan.

The G.A.O. report said that N.I.H. oversight didn’t always ensure that the foreign institutions complied with terms and conditions, including biosafety requirements.

One reason expenditures were hard to track was because of a federal government policy that required reporting subawards only of $30,000 or more, another G.A.O. report said.

That report examined some $48 million in N.I.H. and State Department funding that went to Chinese businesses and research institutions between 2017 and 2021, including one project to study diseases that are transmitted by insects, like malaria.

It found that “the full extent of these subawards is unknown,” and that data was incomplete and sometimes inaccurate, because so many expenditures were exempt from reporting.

Apoorva Mandavilli contributed reporting.