The Defense Department Canceled a Harvard Project’s Grant. Then It Kept Paying.

Updated July 11, 2025, at 6:15 p.m.

The Department of Defense paid Harvard scientists to continue work on their research project, even after the Trump administration said they canceled the grant funding the study, the University claimed in a Friday filing for its lawsuit over the administration’s funding freezes.

The Defense Department sent Harvard a letter on May 12 canceling the award for the project, which focused on identifying new biological threats. But the Defense Advanced Research Projects Agency, the Defense Department unit that funded the project, asked the researchers for samples and an update on their progress well after the grant termination.

And a week after Harvard emailed DARPA’s directors on July 2 asking whether the project’s grant was still active and requesting compensation for the researchers’ work, the University received a full payment of $373,000 from the government.

The University’s Friday filing was an amendment to its motion in June for summary judgment, a process that allows a judge to decide a case without a full trial, in its lawsuit against the Trump administration’s freeze on billions of dollars in federal research funding.

Harvard’s lawyers wrote that the payment provides further support for their argument that the White House’s funding cuts — which have impacted nearly $3 billion in federal grants to the University — were “arbitrary and capricious.”

“DARPA’s conduct is inconsistent with the stated basis for the termination that the AMPHORA award ‘no longer effectuates the program goals or agency priorities,’” the lawyers wrote in reference to the researchers’ project, Assured Microbial Preservation in Harsh or Remote Areas.

A Defense Department cited a policy against commenting on pending litigation and directed inquiries to the Department of Justice. A Justice Department spokesperson did not immediately respond to a request for comment.

The payments were the subject of a dispute within the Pentagon, also made public in Harvard’s court filings. One Defense Department official urged higher-ups to continue the AMPHORA funding, writing that Harvard’s researchers were the program’s “top performing team” and that cutting off the grant posed a “grave and immediate harm to national security.”

The University first sued the Trump administration on April 21 after the government cut an initial $2.2 billion in funding dollars. Since then, the White House has continued to slash research funding, disqualifying the school from future grants and freezing an additional $450 million. Harvard updated its suit in response to the new cuts.

In Harvard’s initial lawsuit, the University’s lawyers argued that the government violated the First Amendment by “imposing viewpoint-based conditions on Harvard’s funding.” They have since accused the Trump administration of failing to follow the procedures for terminating grant funding that are legally required under Title VI of the Civil Rights Act.

Harvard’s lawsuit has drawn widespread support — with 20 states, more than 12,000 alumni, several Jewish advocacy groups, and two dozen universities filing amicus briefs backing the University in its legal effort to wrest back its federal funding from the government.

And that fight is happening in tandem with a second ongoing lawsuit, which the University filed to maintain its ability to enroll international students and updated to contest an entry ban for its international student reentering the United States.

Harvard has won some early victories in this lawsuit. A federal judge granted Harvard a preliminary injunction allowing the school to continue enrolling the students, and a second order blocking the Trump administration’s entry ban for Harvard students.

But despite these wins, the Trump administration’s relentless onslaught has already inflicted serious pain for Harvard and its affiliates. Scientists have said Harvard’s research ecosystem has been thrust into a “survival state” by the funding cuts, and several international students and faculty were turned away at the border — even after the federal judge blocked Trump’s entry ban.

And the White House is continuing to attack the University, serving Harvard a subpoena and threatening its accreditation status Wednesday morning — despite word of reopened negotiations between the two parties, touted publicly by President Donald Trump.

Harvard has denounced the government’s demands as unconstitutional and vowed to maintain its autonomy. But the University has nonetheless taken some steps that mirror the demands, though its leaders have said the changes were made independently and justified in their own right.

Recently, Harvard has walked back its public commitments to diversity, equity, and inclusion — renaming its diversity offices, wiping websites of DEI references, and pulling support for diversity events at Commencement. The changes come as the Trump administration continues to demand that Harvard eliminate its diversity programming or face further punishments from Washington.

—Staff writer William C. Mao can be reached at william.mao@thecrimson.com. Follow him on X @williamcmao.

—Staff writer Veronica H. Paulus can be reached at veronica.paulus@thecrimson.com. Follow her on X @VeronicaHPaulus.