Johns Hopkins joins lawsuit seeking to block cuts to Department of Defense research funding

Johns Hopkins University joined 11 peer research universities along with the American Association of Universities, the American Council on Education, and the Association of Public and Land-Grant Universities in filing a lawsuit in federal court Monday seeking to block significant cuts to research funding by the Department of Defense. The lawsuit was filed in the U.S. District Court for the District of Massachusetts.

In recent memos, Department of Defense leadership announced plans to immediately cap the amount paid for vital indirect costs on all awarded research grants at 15%, a move the DOD estimates will save up to $900 million per year. This follows similar caps on indirect cost rates announced by several federal agencies, including the National Institutes of Health and the National Science Foundation.

On Tuesday, a judge granted a temporary restraining order in the case that prohibits the DOD from implementing the cap. For decades, universities have negotiated with the federal government to determine the reimbursement rates for indirect costs—the real and necessary costs of conducting groundbreaking research that has made our nation the world's leading military superpower. The funds help offset a broad range of costs essential to carrying out research, including equipment and electricity for labs, technical expertise and technological infrastructure, and other basic operational expenses. JHU joined a similar lawsuit in February contesting abrupt cuts to indirect costs by the National Institutes of Health.

"In large part due to the support from and partnership with the federal government, JHU and our research university peers have built and maintained a research ecosystem that nurtures scientific inquiry and technological development, enhances national security, fuels national economic growth and competitiveness, saves and improves lives, and is the envy of the world," Laurent Heller, the university's executive vice president for finance and administration, wrote in a declaration in support of the lawsuit filed Monday. "It has taken many decades for the federal government and research universities together to create this highly effective research ecosystem, but it can be broken and diminished very rapidly if indirect cost funding is dramatically reduced."

Johns Hopkins is a leading partner on defense and national security research projects across a range of areas, including treating traumatic brain injuries and spinal cord injuries in veterans, testing the safety and effectiveness of protective materials under extreme conditions, and developing an AI-based platform for the detection and treatment of heart conditions. The university currently has nearly 300 active Department of Defense grants totaling approximately $375 million across multiple years, with nearly half of that funding going to the School of Medicine and another 39% to the Whiting School of Engineering.

The DOD's strategic investment in research, at Hopkins and across the country, supports technological advancement and innovation with both military and civilian applications. It also creates jobs and long-lasting economic benefits, with many projects training the next generation of scientists and engineers in defense-critical fields.

Through fiscal year 2026, JHU's negotiated indirect cost rate for Department of Defense research grants is 55%. Of the approximately $122 million in DOD funding that the university received in fiscal year 2024, approximately $90 million covered direct costs and approximately $32 million accounted for the DOD's share of indirect costs, with Hopkins co-investing to cover all remaining indirect costs. Johns Hopkins expects to receive similar amounts of DOD funding in fiscal years 2025 and 2026.

If the Department of Defense were to lower its indirect cost reimbursement rate to 15%, contrary to the rate previously negotiated and agreed upon between JHU and the federal government, the university would lose approximately $20 million each year, or about 16% of the funding it receives from the agency.

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The impact of funding cuts

Without research—and the federal support that makes it possible—scientific breakthroughs suffer, and the lifesaving treatments of tomorrow are at risk.

"With funding from DOD, university researchers are making advancements in engineering, tackling complex intelligence challenges, developing state-of-the-art equipment such as undersea weapons, and finding ways to keep our military service members safe on the battlefield," AAU wrote in statement Monday.

"DOD's latest action would have an immediate and dire effect on our national security by disrupting research designed to help our military. It would also harm our universities' ability to continue research in critical emerging technology areas such as artificial intelligence and quantum computing that have significant military applications, and that China is investing in heavily. To put it simply, this cut to university research would make our nation less safe, threaten our future defense readiness, and weaken our global security."

Over the past five months, the federal government has announced terminations, cancellations, or stop work orders affecting research across Johns Hopkins University, including the loss of more than $800 million from U.S. Agency for International Development grant terminations. A further 90 grants from other agencies have been terminated since January, causing the loss of more than $50 million in federal funding for the university's researchers and their teams.