Trump’s Cuts to NIH Indirect Research Funds Blocked by Judge (2)

A federal judge issued a nationwide block against the Trump administration’s moves to slash funds from the National Institutes of Health that cover grant recipients’ research overhead costs, dealing a blow to one of the government’s efforts to reduce spending.

The order issued Wednesday by Judge Angel Kelley of the US District Court for the District of Massachusetts granted states and academic groups their motion for a nationwide preliminary injunction that enjoins the National Institutes of Health from taking any steps to implement a 15% cap on “indirect funds” at the NIH.

The cap on funds applies to research money the government pays to universities and institutions to cover the expenses of facilities, utilities, laboratory equipment, and even project support staff.

The new rate change “impacts thousands of existing grants, totaling billions of dollars across all 50 states—a unilateral change over a weekend, without regard for on-going research and clinical trials,” Kelley wrote on Wednesday.

“The imminent risk of halting life-saving clinical trials, disrupting the development of innovative medical research and treatment, and shuttering of research facilities, without regard for current patient care, warranted the issuance of a nationwide temporary restraining order to maintain the status quo.”

The reduced rate was challenged Feb. 10 by 22 states and other academic membership organizations arguing the cap will have destructive effects on research and walk back decades of progress made by the scientific community. They argued that Trump’s moves violated the Administrative Procedure Act and failed to consider the effects they would have on research.

One of the plaintiffs, the Association of American Medical Colleges, wrote in a statement that they are “heartened that a federal court agreed that critical research funding must continue while the case proceeds.”

“These unlawful cuts would slow medical progress and cost lives, and we will continue our fight to stop the implementation of this harmful action,” David J. Skorton, president of the AAMC, said in a statement. “The AAMC maintains its strong support for robust NIH funding to advance cutting-edge research that benefits every person and community in America.”

The preliminary injunction also ensures that colleges and universities, who are at the “forefront of groundbreaking advancements,” can continue their work without disruption, Dana Nessel, Michigan’s attorney general, wrote in a statement.

The NIH claimed that they aren’t cutting grant funding but rather moving the indirect costs to other funding areas. The agency estimates the reduced rate would save at least $4 billion for the government.

Kelley had already issued and extended a temporary restraining order to block the rate change from going into effect. The judge heard arguments Feb. 21, where she said she had “a lot of work to do,” on deciding whether a preliminary injunction should be issued.

“Even if the Rate Change Notice represented sufficient explanation of policy, procedures, and decision making criteria—of which it includes none—NIH did not comply with the step-by-step process mandated by the language of the regulation,” Kelley wrote Wednesday.

“NIH’s proffered ‘reasons’ fail to grapple with the relevant factors or pertinent aspects of the problem and fails to demonstrate a rational connection between the facts and choice that was made,” Kelley said.

Kelley’s order comes the same day as the confirmation hearing for President Donald Trump’s picks to the lead the NIH, Jay Bhattacharya, before the Senate Committee on Health, Education, Labor and Pensions.

Senators pressed Bhattacharya on his plans for the cap on indirect costs, but he wouldn’t address them. “There’s a lot of distrust about where that money goes, because the trust in the public health establishment has collapsed since the pandemic,” Bhattacharya told the Senate panel.

The NIH did not immediately respond to request for comment.

The case is Commonwealth of Massachusetts v. NIH, D. Mass., No. 1:25-cv-10338, 3/5/25.