A federal judge ordered the Trump administration to hold off on a plan that would cut $4 billion in federal funding for research at the nation’s universities, cancer centers and hospitals.
The funds disbursed by the National Institutes of Health cover the administrative and overhead costs for a vast swath of biomedical research, some of which is directed at tackling diseases like cardiovascular conditions, cancer and diabetes.
The order was issued by Judge Angel Kelley for the U.S. District Court in Boston late Monday night in response to a lawsuit filed by university associations and major research centers that had argued that the “flagrantly unlawful action” by U.S. health officials “will devastate medical research at America’s universities.”
The temporary restraining order by Judge Kelley, a Biden appointee, expanded on a similar order that was granted earlier Monday after nearly two dozen attorneys general sued to stop the cuts in their states.
The Trump administration’s plan to cap agreed-upon payments that universities and health systems receive to support research rocked the academic medical world when it was abruptly announced Friday.
Academic researchers and university officials predicted that the plan would shut down valuable studies, cost thousands of jobs and kneecap the United States in competitive efforts to achieve medical breakthroughs.
The plan applied to $9 billion of the $35 billion in grants issued to research institutions. That quarter of the total research funding supports so-called indirect costs that apply to expenses for administrative overhead, including, for example, staff and building or lab operations and maintenance.
The Trump administration said it wanted to cut such funds roughly in half, by about $4 billion.
The funding for overhead costs has been criticized in the past. And opposition to the funds emerged in the Project 2025 blueprint for conservative policies, suggesting that the N.I.H. research funding gave too much support to “leftist” universities.
On Friday, Katie Miller, a member of the effort by Elon Musk to slash the size of the federal government, posted on social media: “President Trump is doing away with Liberal D.E.I. Deans’ slush fund.”
Universities hold a starkly different view. The funds support scientific breakthroughs that “are becoming more frequent and more consequential,” Dr. Alan M. Garber, the president of Harvard University, said in a statement on Sunday.
“At a time of rapid strides in quantum computing, artificial intelligence, brain science, biological imaging and regenerative biology, and when other nations are expanding their investment in science, America should not drop knowingly and willingly from her lead position on the endless frontier,” Dr. Garber said.
The plaintiffs, including the Association of American Medical Colleges and the American Association of Colleges of Pharmacy, claimed that the sudden funding cut would “wreak havoc” on critical research and ultimately force universities to lay off staff, close laboratories and shutter certain research programs altogether.
In a legal memo related to the lawsuit, universities argued that the funds were indispensable in research, including at facilities where lab animals undergo clinical testing, for the computer systems that analyze large amounts of data, for blood banks and other expenses that cannot be directly tied to a single project.
If the funding cutbacks were to survive legal challenges, the plaintiffs wrote, “research laboratories would literally go dark for lack of electricity.”
Smaller institutions, they argued, might not be able to sustain any research and “could close entirely.”
Congress thwarted an earlier effort during the first term of President Trump to cut indirect research funding. Lawmakers added measures to budget bills to ensure that the funds remained at the levels agreed upon by researchers and federal officials.
In the lawsuit, the association of universities argued that the current proposal violated the will of Congress and also defied standard administrative procedures.
In granting the temporary halt to the cutbacks, Judge Kelley ruled that the plaintiffs would “sustain immediate and irreparable injury.”
A hearing date was set for Feb. 21.
