Judge temporarily blocks NIH research cuts after 22 states sue

Jessie Hellmann and Sandhya Raman, CQ-Roll Call on Feb 10, 2025

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WASHINGTON — A federal judge in Massachusetts late Monday granted a temporary restraining order blocking the Trump administration’s cuts to National Institutes of Health research funding after 22 states filed a lawsuit challenging that order.

District Court Judge Angel Kelley of the U.S. District of Massachusetts gave the administration until Friday to file an opposition to the motion and scheduled a hearing for Feb. 21.

The lawsuit, filed Monday in the United States District Court for the District of Massachusetts, seeks to block a change by the National Institutes of Health that would cut payments to universities, medical centers and researchers studying cancer, rare diseases and other health issues.

That announcement, made on Friday, would limit the indirect costs it will pay grantees to 15 percent of a grant.

The cuts took effect early Monday and appear to be part of President Donald Trump’s efforts to reduce federal spending without congressional approval.

“Massachusetts is the medical research capital of the country,” said Massachusetts Attorney General Andrea Joy Campbell, whose state received approximately $3.46 billion in appropriations to 219 organizations through NIH in fiscal 2024. “We will not allow the Trump Administration to unlawfully undermine our economy, hamstring our competitiveness, or play politics with our public health.”

The lawsuit was filed by 22 states known for being powerhouses of biomedical research, including Massachusetts, California, Maryland and New York.

Also part of the lawsuit are: Michigan, Illinois, Arizona, Connecticut, Colorado, Delaware, Hawaii, Maine, Minnesota, Nevada, New Jersey, New Mexico, North Carolina, Oregon, Rhode Island, Vermont, Washington and Wisconsin.

The Trump administration’s new cap will “devastate critical public health research at universities and research institutions in the United States,” the lawsuit claims. “Without relief from NIH’s action, these institutions’ cutting-edge work to cure and treat human disease will grind to a halt.”

The NIH is the primary source of federal funding for medical research in the U.S., spending more than $45 billion on 50,000 competitive grants in fiscal 2023. About $26 billion of that went to direct research costs while $9 billion went to indirect costs that year, according to NIH in supplemental guidance Friday.

Universities and medical institutions are the main beneficiaries of these grants, which are used to study diseases like cancer, study public health threats, run clinical trials and much more.

The funds are crucial to covering costs “essential” for research, including administrative costs, clerical staff, IT support, cybersecurity and data repositories, and more, the lawsuit argues.

The lawsuit claims the cuts will harm the states’ citizens who will be “adversely affected” by the “halting of research involving a better understanding of health conditions.”

“These universities and research institutions are vital economic and social institutions in each state, employing thousands of their citizens, educating and training thousands more, and creating investment and partnering opportunities with the private sector,” the lawsuit states.

“Let’s be clear about what they are seeking to do now: they want to eviscerate funding for medical research that helps develop new cures and treatments for diseases like cancer and Alzheimer’s,” said California Attorney General Rob Bonta. “I will not allow the Trump Administration to jeopardize the extraordinary work being done right now by scientists, scholars, medical professionals, and other workers.”

Before Monday, a grantee’s indirect-costs rate was negotiated directly between the federal government and research institutions. The amount received varies widely between institutions, with the NIH highlighting Friday that prestigious universities like Harvard received indirect costs as high as 69%.

The NIH claimed the change would save $4 billion immediately, but did not indicate whether that funding would be funneled into more research.

“The United States should have the best medical research in the world. It is accordingly vital to ensure that as many funds as possible go towards direct scientific research costs rather than administrative overhead,” the NIH said in the supplemental guidance.

The lawsuit argues the change violates federal law, citing an appropriations rider, first added in 2018, prohibiting the Department of Health and Human Services or NIH from spending appropriated funds to implement changes to the reimbursement of indirect costs.

“This agency action will result in layoffs, suspension of clinical trials, disruption of ongoing research programs and laboratory closures,” the lawsuit claims.

The change is also illegal because NIH didn’t go through the federal rulemaking process, nor did it articulate the basis for a 15% cap, the lawsuit argues.

Congressional response

Senate Appropriations Chair Susan Collins, R-Maine, in a statement Monday rebuked the “poorly conceived directive” at NIH.

She said that she had also spoken to Robert F. Kennedy, Jr, the nominee for HHS secretary, and had received his assurance that he would reexamine this move after he is confirmed.

“There is no investment that pays greater dividends to American families than our investment in biomedical research,” said Collins, who said she has heard from at least five biomedical research institutions in her state with concerns. “Additionally, Fiscal Year 2024 Appropriations legislation includes language that prohibits the use of funds to modify NIH indirect costs.”

Collins’ state is among those that sued the Trump administration Monday. The University of Maine System had negotiated indirect-costs rates between 26% and 47.7%, according to the lawsuit. The NIH’s reduction to 15% will eliminate $1.4 million in anticipated funding.

Rep. Andy Harris, R-Md., criticized the uproar over the cuts.

“The NIH’s new indirect cost rate of 15% is in line with what research institutions receive from private foundations, and could actually allow more NIH funding to go directly to critical scientific research,” said Harris, a member of the House Labor-HHS-Education Appropriations Subcommittee, echoing arguments made by the Trump administration.

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