“The pace of scientific discoveries in the national interest will be slowed,” according to the court filing. “Progress on a safe and effective nuclear deterrent, novel energy sources, and cures for debilitating and life-threatening illness will be obstructed. America’s rivals will celebrate, even as science and industry in the United States suffer.”
The universities asked a federal judge in Boston to immediately block the Trump administration from moving forward with the policy change. These indirect research expenses include electricity, money for lab equipment, staff, and more, according to the complaint.
DOE grants support the work of nearly 1,000 people at MIT, president Sally Kornbluth wrote in a statement.
Cornell University, Princeton University, California Institute of Technology, Michigan State University, University of Michigan, University of Illinois, University of Rochester, the Association of American Universities, the American Council on Education, and the Association of Public and Land-Grant Universities are also listed as plaintiffs in the case.

The energy department announced last week that it would cap its annual reimbursement rate of “indirect costs” of department research to 15 percent. The average rate of indirect costs at universities is currently more than 30 percent, according to a government press release. This cut is poised to generate more than $405 million in annual cost savings, the department said.
“The purpose of Department of Energy funding to colleges and universities is to support scientific research — not foot the bill for administrative costs and facility upgrades,” US Secretary of Energy Chris Wright said in a statement.
In a joint statement, officials from the AAU, the APLU, and the ACE said these cuts would have a “dire impact on critical energy, physical sciences and engineering research nationwide.”
“It also sets a very dangerous precedent that could be used to undermine federal investments in research at many other federal agencies,” the statement said.
Brown president Christina H. Paxson said the university will continue to take whatever action necessary to protect funding that supports Brown’s research and “our country’s need for innovative solutions to critical problems.” She said the energy department’s cuts are in areas that are key to the nation’s current and future energy needs and security, “as well as the technology and innovation required to maintain America’s global leadership.”
Areas of research funded by the energy department at Brown include artificial intelligence, quantum information science, and nuclear technology — all of which have been identified as critical priorities of the current federal administration.
The proposed cuts could mean Brown will be forced to eliminate positions that support research and facilities.
“Without the opportunity to conduct this research, skilled faculty will opt to leave Brown, and likely the United States, in pursuit of viable work,” said Greg Hirth, Brown’s vice president for research, in a court filing. “This brain-drain will inevitably lead to lost opportunities to develop US intellectual property, advance American science and energy security, create US startup companies, and develop a workforce critical for the science and technical priorities of the current administration.”
Similar to its Ivy League colleagues, Brown has been under increased scrutiny by the Trump administration. Last week, university officials confirmed that the US Department of Health and Human Services said it would expand its probe of alleged antisemitism at a May 2024 protest to include all of Brown University going back to October 2023. That action comes as the Trump administration has confirmed to the Globe — but has yet to contact the university — that it will block $510 million in federal contracts and grants for Brown as part of its push to hold elite universities accountable for persistent antisemitism on campus.
Millions in public health research funding has also been cut at Brown since Trump’s inauguration. Hundreds of faculty members have organized, and requested that the university’s leadership and governing body stand up and fight against the president’s tactics.
In Cambridge, MIT has imposed an immediate hiring freeze on “all nonessential positions,” excluding faculty, due to the uncertainty in Washington. Similar to Brown, it also filed a suit against the Trump administration, alleging that cuts to indirect costs on the National Institutes of Health grants were unconstitutional. The court granted a permanent injunction, which has remained in place while the federal government seeks to appeal.
This story has been updated with comments from Christina Pasxon and Greg Hirth.
Alexa Gagosz can be reached at alexa.gagosz@globe.com. Follow her @alexagagosz and on Instagram @AlexaGagosz.