A federal judge in Boston granted on Monday a temporary restraining order sought by Maine Attorney General Aaron Frey and attorneys general from 21 other states to stop the Trump administration from cutting medical research funding, including to institutions such as Jackson Laboratory, University of New England and University of Maine.

The restraining order temporarily bars the cuts in the 22 states, but they are still in effect in the other states.

Sen. Susan Collins, R-Maine, criticized the new limit on research funding, saying it could disrupt life-saving biomedical research, including ongoing work taking place in laboratories in Maine.

Maine Attorney General Aaron Frey. Gregory Rec/Portland Press Herald, file

On Friday, the National Institutes of Health announced that it would limit the amount of grant funding that can be used by medical and public health institutes to cover indirect costs associated with their research, including utility costs, equipment, staff and other infrastructure.

Those indirect costs, or overhead, have traditionally been negotiated by the researchers and the federal government. The NIH said on social media that on average about 28% of its grant funding is spent on overhead.

The NIH said Friday that no more than 15% of any research grant could be spent on the indirect costs. Recipients spending more than 15% would see their funding reduced.

The NIH said the new cap would save $4 billion a year.

“Contrary to the hysteria, redirecting billions of allocated NIH spending away from administrative bloat means there will be more money and resources available for legitimate scientific research, not less,” White House spokesman Kush Desai wrote in an email to the Washington Post.

The order took effect Monday, leaving little time for affected institutions to respond.

The University of New England stands to lose about $2 million a year for research into Alzheimer’s disease, dementia, drug development and chronic pain, among other things, UNE President James Herbert said.

“They would also reduce the number of students — the scientists of tomorrow – who are in training,” he said. “It is not an exaggeration to say that these cuts threaten to jeopardize U.S. dominance in biomedical research for years to come. We are fortunate in Maine to have an engaged Congressional delegation that appreciates how short-sighted these cuts would be to the state and indeed the nation.”

The cap would lead to a nearly $1.4 million cut to current research projects for the University of Maine System, plus an additional $6.2 million in cuts in pending research requests, a spokesperson said.

The NIH spends nearly $8.8 million on 23 research projects in the university system, which also has an additional $29 million in pending funding requests for 26 more projects.

University spokesperson Samantha Warren said facilities and administration costs are “foundational for research” and “essential expenses,” including meeting compliance guidelines, maintaining campus laboratories and protecting discoveries from foreign adversaries.

“There is a cost of doing research, and when our public universities conduct research on the federal government’s behalf, the federal government appropriately pledges to pay a portion of our necessary costs,” Warren said in an email.

Current funding at risk

“Setting aside the feasibility of conducting future research, walking back funding promises on activity already underway weakens Maine’s largest research enterprises, reduces access to hands-on learning opportunities for Maine students, and threatens the development of Maine-made cures, including for cancer, heart disease, infectious diseases and neuromuscular disorders,” Warren continued.

Frey joined 21 other attorneys general in the lawsuit filed Monday in U.S. District Court in Massachusetts against the administration, NIH, and the U.S. Department of Health and Human Services “to block this unlawful attempt to cut NIH funding.”

“The NIH funds critical public health research throughout the country and right here in Maine,” Frey said. “While the drastic slashing of this funding is being branded an ‘overhead’ savings, it in fact threatens to cripple vital research into areas that touch the lives of many Mainers, including cancer treatment, infectious diseases, neuromuscular disorders, aging and addiction. The loss of NIH funds will also impact Maine-based organizations that employ Mainers and attract new talent to our state.”

The lawsuit argues that the NIH directive capping indirect costs violates the Administrative Procedure Act, which Frey said prohibits the NIH from requiring “categorical and indiscriminate changes to indirect cost reimbursements.”

Other states joining the lawsuit are: Arizona, California, Colorado, Connecticut, Delaware, Hawaii, Illinois, Maryland, Massachusetts, Michigan, Minnesota, Nevada, New Jersey, New Mexico, New York, North Carolina, Oregon, Rhode Island, Vermont, Washington and Wisconsin.

Collins speaks out

Collins also spoke out against the cap Monday, saying the “poorly conceived” directive could hurt researchers at institutions such as Jackson Lab, Maine Medical Center Research Institute, University of Maine, University of New England and MDI Biological Laboratory. These groups warned about a stoppage of research and job losses, she said.

“There is no investment that pays greater dividends to American families than our investment in biomedical research,” Collins said in a written statement. “In Maine, scientists are conducting much-needed research on Lyme disease and other tick-borne illnesses, Alzheimer’s, diabetes, Duchenne muscular dystrophy, and on how to improve efficiency in drug discovery, helping to lower the cost of prescription drugs, and conducting many other life-enhancing or life-saving research.”

Sen. Susan Collins, R-Maine. Mariam Zuhaib/Associated Press, file

Collins noted that lawmakers have already passed a law prohibiting the NIH from modifying rules regarding indirect costs.

The senator said she spoke Monday morning with Robert F. Kennedy Jr., who has been nominated to lead the U.S. Department of Health and Human Services. She said Kennedy — who could face a Senate confirmation vote this week — told her that he plans to take a second look at “these arbitrary cuts … as soon as he’s confirmed.”

The lawsuit is the latest to be filed by Maine and other states asking the courts to push back on the Trump administration’s flurry of executive orders the last three weeks, which have sought to end birthright citizenship, unilaterally freeze federal grants and loans, and shut down entire agencies.

It also comes as billionaire businessman Elon Musk and his team, known as the Department of Government Efficiency, are moving aggressively to cut federal spending and reshape the federal workforce.

Such actions have led to widespread confusion and fear, as constituents here and elsewhere have flooded phone lines, raising concerns among Maine’s delegation about the amount of power Trump has ceded to Musk, who was not vetted through any confirmation process.

Separation of powers jeopardized?

Trump’s moves, especially his administration’s effort to unilaterally cut programs and funding authorized by Congress, have raised concerns about a constitutional crisis that could upend one of the country’s founding principles, having three separate and co-equal branches of government, and place more power with the presidency.

Last week, Congress confirmed Russell Vought as the White House budget chief. He believes that a 1974 law enacted by Congress requiring the president to spend congressionally approved funding is unconstitutional.

Collins, who traveled with other Republican senators to meet with Trump at Mar-a-Lago in Florida on Friday, voted in support of Vought — even though she said she disagrees with his views on withholding congressionally approved funding, known as impoundment.

So far, the courts have stopped several of the Trump administration’s initiatives from moving forward, at least temporarily.

Maine has now joined a total of four lawsuits against the Trump administration. In addition to the research funding conflict, Frey has challenged efforts to end birthright citizenship and gender-affirming care, and challenged Musk’s access to sensitive personal information.