A federal judge temporarily halted the Trump administration’s radical changes to how the National Institutes of Health pays for biomedical research, putting on hold a plan to slash research funding paid out by the federal government.
Twenty-two state attorneys general filed a lawsuit Monday against the plan, which would limit how it pays out universities and research institutes for “indirect costs.”
The lawsuit, which lists both the National Institutes of Health and the Department of Health and Human Services as defendants, said the effect of the indirect rate changes announced Friday would be “immediate and devastating.”
NIH announced Friday that it would limit indirect funding for research projects to 15%, dramatically slashing how much funding the federal government would provide to research agencies for things like equipment, maintenance, utilities and support staff. Previously, such rates varied and were negotiated by each institution with the government. The new policy took effect Monday for all new NIH grants and any new expenses on existing grants.
The lawsuit, filed Monday in U.S. District Court in Massachusetts and led by attorneys general in Massachusetts, Illinois and Michigan, claims that NIH violated the Administrative Procedure Act, which governs the process of how federal agencies develop and issue new regulations. It also claims that the administration ignored the will of Congress, which has included a provision designed to prevent changes to indirect cost rates since 2018 and after President Donald Trump’s first administration tried to alter the process.
Angel Kelley, a U.S. district judge, granted the attorneys generals’ request for a temporary restraining order, ordering the agencies not to take any steps to implement, apply or enforce the new policy. Kelley set an in-person hearing for Feb. 21.
Kelley is requiring the agencies to file reports, the first of which is due within 24 hours, to confirm that they are continuing to provide grant funds and taking steps to comply with the restraining order, according to court documents.
Earlier Monday in a separate case, a Rhode Island federal judge ruled that the Trump administration had violated his order to stop a federal funding freeze.
Every state with a Democrat serving as the attorney general is part of the new lawsuit.
“This agency action will result in layoffs, suspension of clinical trials, disruption of ongoing research programs, and laboratory closures,” the lawsuit says. “NIH’s extraordinary attempt to disrupt all existing and future grants not only poses an immediate threat to the nation’s research infrastructure, but will also have a long-lasting impact on its research capabilities and its ability to provide life-saving breakthroughs in scientific research.”
The National Institutes of Health directed an NBC News request for comment to the Department of Health and Human Services, which did not provide a comment for publication.
Scientists have described the cuts to indirect costs as draconian and something that would almost certainly stymie research efforts on diseases and for basic science that could lead to new discoveries.
“This is going to have a bad effect on research. If you don’t want research to happen, you can accomplish it this way,” said Michael Eisen, a professor and biologist at the University of California, Berkeley.
Limiting indirect costs would likely shift the burden of funding research away from the federal government and toward universities and individual research institutions, and many have said they don’t have the funding to support it.
In a news release, the University of California system said NIH is the largest funder of its research and spent $2.6 billion on the system’s research during the last academic year. NIH’s changes would cut hundreds of millions from the University of California budget annually.
“This imprudent action will result in immediate broad reductions of personnel and services, including impacts on education, training, delivery of care to patients, basic research, and clinical trials,” said Theresa Maldonado, the University of California system’s vice president for research and innovation. “It will be disruptive for a prolonged period, permanently damaging time-sensitive work in both basic and clinical research.”
Proponents of the NIH shift have described indirect costs as out-of-control overhead costs.
In a post Friday on X, Katie Miller, an appointee to the newly formed Department of Government Efficiency, or DOGE, wrote: “President Trump is doing away with Liberal DEI Deans’ slush fund. This cuts just Harvard’s outrageous price gouging by ~$250M/ year.”