Federal Judge Temporarily Blocks NIH Cuts to Federal Medical Research Funding

WASHINGTON — A federal judge in Massachusetts has temporarily barred the Trump administration from carrying out steep cuts to medical research grants funded by the National Institutes of Health.

The two-page order issued by U.S. District Judge Angel Kelley Tuesday afternoon doesn’t disclose a rationale for the move, but directs the NIH and the Department of Health and Human Services to provide status reports to the court beginning on Wednesday and biweekly thereafter, confirming the government is continuing to disburse federal assistance funds.

Attorneys general in 22 states sued the Trump administration on Monday in a bid to block steep cuts to medical research grants funded by the NIH.

The lawsuit filed in federal court in Massachusetts is a response to the NIH’s announcement Friday that it will limit the amount it pays for the “indirect costs” of research to just 15% of a grant.

In their 59-page complaint, the attorneys general claim the new cap on pay for everything from facilities and their maintenance to clerical staff and IT support will “devastate critical public health research at universities and research institutions.”

“Without relief from NIH’s action, these institutions’ cutting-edge work to cure and treat human disease will grind to a halt,” the complaint says.

In a written statement, Massachusetts Attorney General Andrea Joy Campbell, who is co-leading the lawsuit, described her state as “the medical research capital of the country.”

It’s certainly in the running, having received almost $3.5 billion through the NIH in 2024, money that was allocated to 219 different research organizations.

Overall, to lend some perspective to the numbers, the NIH said it provided about $45 billion in competitive grants the year before that, about $26 billion of which covered direct research costs and $9 billion in indirect costs.

“We are the proud home of nation-leading universities and research institutions that save lives, create jobs and help secure a better future,” Campbell said.

Given the stakes, she vowed she would not “allow the Trump administration to unlawfully undermine our economy, hamstring our competitiveness or play politics with our public health.”

But the White House believes such concerns are overblown.

According to the administration, the new indirect costs policy is intended to bring federal funding into line with what research institutions receive from private foundations. 

“The indirect cost rate is intended to cover overhead and the federal government has been paying an exorbitantly high rate,” a release from the White House Office of Communications said earlier this week.

The NIH itself says the average indirect cost rate it has paid out over time has averaged between 27% and 28% — and many organizations are much higher, charging indirect rates of over 50% and in some cases over 60%. 

“Most private foundations that fund research provide substantially lower indirect costs than the federal government, and universities readily accept grants from these foundations,” the White House said. “For example, a recent study found that the most common rate of indirect rate reimbursement by foundations was 0%, meaning many foundations do not fund indirect costs whatsoever.”

In addition, it noted, many of the nation’s largest funders of research — such as the Bill and Melinda Gates Foundation — have a maximum indirect rate of 15%.  

And in the case of the Gates Foundation, the maximum indirect costs rate is 10% for institutions of higher education.

“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 imposing the new rate.

In addition to Massachusetts, other states participating in the lawsuit are Arizona, California, Colorado, Connecticut, Delaware, Hawaii, Illinois, Maine, Maryland, Michigan, Minnesota, Nevada, New Jersey, New Mexico, New York, North Carolina, Oregon, Rhode Island, Vermont, Washington and Wisconsin.

After the court issued its restraining order, California Attorney General Rob Bonta said he was pleased by its intervention.

“The Trump administration unlawfully sought to eviscerate funding for medical research, and they are now blocked from doing so,” Bonta said.

“My fellow attorneys general and I will be closely monitoring to ensure that the Trump administration follows the court’s order,” he continued. “Public and private universities in California are doing lifesaving research that would otherwise be disrupted.”

Dan can be reached at [email protected] and @DanMcCue