Trump Administration Calls for Harvard Funding Freeze to Be Reinstated, Says Cuts Were Lawful

The Trump administration called on the First Circuit to reinstate its roughly $2.7 billion freeze on Harvard’s research funding, arguing that it acted within its authority when it terminated the University’s grants.

In a 160-page brief filed on Wednesday, federal lawyers laid out their most comprehensive defense yet of the funding cuts, contending that agencies can revoke support based on shifting “agency priorities” — including concerns about antisemitism — even outside the formal enforcement process required under Title VI.

The filing asks the court to overturn a September ruling by U.S. District Judge Allison D. Burroughs, who found the administration’s actions unconstitutional and ordered the funding restored. Harvard announced weeks later that nearly all of the frozen funds had returned to its coffers.

A Harvard spokesperson wrote in a statement that the government’s brief failed to “supply any legitimate basis for cutting off critical research funding” and said it would continue to fight against “the government’s retaliatory campaign.”

“The government’s brief does little to challenge the district court’s exhaustive analysis and it reinforces that the government’s actions are a direct threat to academic freedom,” the spokesperson added.

At its core, the administration’s appeal rests on three claims: that Burroughs lacked jurisdiction to block the cuts, that Title VI does not provide the exclusive mechanism for terminating federal funds over discrimination concerns, and that the government did not violate the First Amendment through its April 2025 demand letter to Harvard.

First, the administration argued that Harvard’s lawsuit was filed in the wrong court altogether. Because the dispute stems from terminated grant agreements, they wrote, it belongs in the Court of Federal Claims rather than federal district court — even if Harvard casts its challenge in constitutional terms.

Second, the administration disputed a central premise of Burroughs’ ruling: that Title VI provides the pathway for cutting off federal funds over allegations of discrimination. Instead, federal lawyers argued that agencies retain authority under the terms of grant agreement to terminate funding when it no longer “effectuate program goals.”

Accepting Burroughs’ interpretation, the brief argued, would create an “absurd” system in which institutions accused of discrimination received greater procedural protections than other federal contractors.

Finally, the government defended its actions against Harvard’s First Amendment claims. Federal lawyers argued that the government did not unlawfully coerce the University when it sought “voluntary resolution of its concerns” through an April 2025 demand letter to Harvard that outlined potential conditions for continued funding.

In her September ruling, Burroughs argued that the letter’s demands had little to do with combatting antisemitism and instead sought to attack Harvard on the basis of its “power and political views.”

Though the government’s lawyers acknowledged that “some proposals” in the letter may have infringed on Harvard’s independence, they contended that “the overwhelming majority” were concerned with legitimate grievances about antisemitism and discrimination at Harvard.

And even if some elements touched protected conduct, the brief argued, the administration would have reached the same funding decision regardless.

“To the extent the reforms implicated protected conduct, it did so only incidentally to address the root problems of unlawful discrimination and failure to address antisemitism,” the government’s lawyers wrote.

The Trump administration first appealed the ruling in December, meeting its deadline for a formal brief on Wednesday. In the filing, federal lawyers also requested oral argument, writing that the case raises “significant issues” about the scope of federal funding authority and civil rights enforcement.

—Staff writer Hugo C. Chiasson can be reached at [email protected] or on Signal at hcc.35. Follow him on X @HugoChiassonn.

—Staff writer Elise A. Spenner can be reached at [email protected] or on Signal at elisespenner.82. Follow her on X @EliseSpenner.