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.