Nearly two dozen states sued the Trump administration and the National Institutes of Health on Monday to block a $4 billion cut to research funding that scientists say would cost thousands of jobs and eviscerate studies into treatments for cancer, Alzheimer’s, heart disease and a host of other ailments.
The funding cuts were to take effect Monday. The attorneys general of Massachusetts and 21 other states filed the suit, arguing the Trump administration’s plan to slash overhead costs — known as “indirect costs” — violates a 79-year-old law that governs how administrative agencies establish and administer regulations.
“Without relief from N.I.H.’s action, these institutions’ cutting-edge work to cure and treat human disease will grind to a halt,” the lawsuit said.
On Capitol Hill, Senator Susan Collins of Maine, the chairwoman of the chamber’s Appropriations Committee, strongly objected to what she called “these arbitrary cuts.” Ms. Collins, a Republican, said that when she called President Trump’s nominee for health secretary, Robert F. Kennedy Jr., to complain, he promised to “re-examine this initiative” if confirmed.
The filing is the latest in a string of lawsuits challenging Mr. Trump’s policies. Also on Monday, a federal judge in Rhode Island ordered the Trump administration to “immediately restore” trillions of dollars in federal grants and loans, including from the N.I.H., that had been frozen under a sweeping directive the president issued, and later rescinded, late last month.
Scientists, medical researchers and public health officials have felt under siege since Mr. Trump became president. In addition to freezing grant dollars and slashing overhead costs, the administration has blocked the Centers for Disease Control and Prevention from publishing scientific information on the threat of bird flu to humans.
The lawsuit filed Monday involves a change, announced Friday by the N.I.H., in the formula that the government uses to determine the share of grant dollars that can go toward overhead costs. Those expenses include lighting, heating and building maintenance, but also the upkeep of sophisticated equipment that is too expensive for any single laboratory to buy on its own.
The plan would cost the University of California system hundreds of millions annually, the system’s president, Dr. Michael V. Drake, said.
“A cut this size is nothing short of catastrophic for countless Americans who depend on U.C.’s scientific advances to save lives and improve health care,” Dr. Drake said in a statement Monday. “This is not only an attack on science, but on America’s health writ large. We must stand up against this harmful, misguided action.”
State officials are also concerned that the cuts could harm their economies. Massachusetts prides itself on being the “medical research capital of the country,” the state attorney general, Andrea Joy Campbell, a Democrat, said in announcing the suit, adding, “We will not allow the Trump administration to unlawfully undermine our economy, hamstring our competitiveness, or play politics with our public health.”
The N.I.H. awarded $4.5 billion in research funds in Massachusetts in recent years, including for research on pancreatic cancer, hypertension and severe asthma. The N.I.H. also sent about $5 billion to New York. The cut is expected to cost the state about $850 million, the lawsuit said.
Last year, the N.I.H. said, $9 billion of $35 billion — or about 26 percent — of grant dollars it distributed went to overhead, or indirect costs. Some academic institutions devote 50 percent or more of their grant dollars to such costs. But the new policy would cap these “indirect funds” at 15 percent, saving $4 billion, the administration said.
Slashing indirect funds was a goal of Project 2025, a set of right-wing policy proposals put forth by the Heritage Foundation as a blueprint for a second Trump administration. The project’s report said the cuts “would help reduce federal taxpayer subsidization of leftist agendas.”
Administration officials and their allies cast the indirect costs as a taxpayer giveaway to elite universities whose large endowments, or outside funding from private foundations, could easily cover those costs.
“President Trump is doing away with Liberal DEI Deans’ slush fund,” Katie Miller, a member of the Elon Musk-led effort to slash the size of the federal government, wrote Friday on social media. “This cuts just Harvard’s outrageous price gouging by ~$250M/ year.”
But Lawrence O. Gostin, an expert in public health law at Georgetown University, said that many smaller academic institutions, including historically Black colleges and universities, do not have extra funds to cover those costs, and would have to scale back medical research if the 15 percent cap remained intact.
An N.I.H. spokeswoman referred questions to its parent agency, the Department of Health and Human Services, which is also named as a defendant in the lawsuit. The department declined to comment, citing the pending litigation.
This is not the first time a Trump administration has moved to cut the funds. In 2017, during Mr. Trump’s first term, a similar proposal would have reduced the overhead payments to 10 percent of the award amount, according to Monday’s lawsuit. The effort faltered.
Congress then acted to “ward off” a future effort and passed a budget bill that prohibited changing the fees from the levels that had been negotiated between federal officials and each research institution, according to the lawsuit.
People familiar with the negotiations said those deliberations are complex, lengthy affairs that involve costs for items like heating bills and personnel, backed by binders full of supporting records. The lawsuit claims that the administration cannot make indiscriminate changes to the action that Congress took. It also said the notice announcing the rate change violated the Administrative Procedure Act in multiple ways.
The proposed changes have been jarring to universities, which had already finalized budgets assuming that the funds would arrive. The changes were announced Friday and were to take effect Monday.
“There just isn’t anywhere near that much discretionary money floating around anywhere,” said Jeremy Berg, a former N.I.H. division director who oversaw general medical research. “The only thing that a university could do is do less research and start firing staff and faculty. And it would be devastating.”
The cuts’ largest effect would hit the University of California system, which the lawsuit said gets $2 billion in N.I.H. research funds for numerous universities and cancer treatment centers. The funds have supported groundbreaking research there, including the invention of gene editing and the first radiation treatment for cancer, according to the lawsuit.
While lawsuits against the Trump administration have tended to be dominated by Democratic-led states, this case also has places that more recently favored Mr. Trump in the election.
They include North Carolina, which gets about $3.7 billion in N.I.H. research funding awarded to schools like Duke, the University of North Carolina and Wake Forest. Dr. Robert Lefkowitz, who is a professor of medicine at Duke and a recipient of the Nobel Prize in Chemistry, said in an interview over the weekend that “a lot of research will just have to stop” if the cuts go through.
“I can’t imagine a better use of taxpayer money,” he said of the funding.
Michigan, a presidential swing state that Mr. Trump carried in November, also sued, citing a probable loss of $181 million in funding to the University of Michigan alone. The lawsuit said the university has 425 N.I.H.-funded trials underway focused on several diseases, “including 161 trials aimed at saving lives.”
The lawsuit also included the presidential battlegrounds of Arizona, Nevada and Wisconsin. The cuts, according to the lawsuit, would carve $65 million from the budget of the University of Wisconsin at Madison, which is studying adult and pediatric cancer, diabetes and degenerative neurological diseases and other conditions.
