In a sharp rebuke to the Trump administration’s budget-slashing ambitions, a federal judge in Boston has thrown a legal wrench into the Defense Department’s move to dramatically cut research funding for universities across the country.
U.S. District Judge Brian Murphy issued a temporary restraining order halting the Pentagon’s recently adopted 15% cap on indirect cost reimbursements for academic research—an accounting maneuver that, if left unchecked, would have pulled the financial rug out from under dozens of institutions reliant on federal grants.
The lawsuit, spearheaded by a dozen top-tier universities including MIT and Johns Hopkins, along with the Association of American Universities and other academic consortia, paints the cap as not just harmful—but unlawful. The plaintiffs argue that the Defense Department’s unilateral policy shift disregards established federal regulations and defies Congressional intent.
These “indirect costs” aren’t just bureaucratic fluff—they help pay for lab maintenance, research infrastructure, and technical staff, the hidden machinery powering groundbreaking scientific work.
The Defense Department, under Secretary Pete Hegseth, pitched the cuts as a fiscal belt-tightening measure that could save up to $900 million annually. But to researchers and universities, it was a guillotine disguised as a scalpel.
This legal clash is part of a broader pattern: other federal agencies like the National Institutes of Health and Department of Energy have tried similar moves, only to be blocked by courts in the same jurisdiction.
Judge Murphy, a Biden-era appointee, has set a follow-up hearing for July 2, where a longer-lasting injunction could be on the table. Until then, the administration’s attempt to squeeze universities dry has been placed on ice.
The government offered no immediate comment as it prepares for the courtroom showdown.
