The US Justice Department filed a new lawsuit Friday against Harvard University, saying its leadership failed to address antisemitism on campus, creating grounds for the government to freeze existing grants and seek repayment for grants already paid.

The lawsuit, filed in federal court in Massachusetts, is another missive in a protracted battle between the administration of US President Donald Trump and the elite university. In the complaint, the US Justice Department accused Harvard of remaining deliberately indifferent to hostility on its campus and has intentionally refused to enforce its campus rules when victims are Jews or Israelis.

“This sent the clear message to Harvard’s Jewish and Israeli community that the indifference was not an accident; they were being intentionally excluded and effectively denied equal access to educational opportunities,” the complaint said.

“The United States cannot and will not tolerate these failures and brings this action to compel Harvard to comply” with federal civil rights law, the Justice Department continued, “and to recover billions of dollars of taxpayer subsidies awarded to a discriminatory institution.”

In response, Harvard called the lawsuit “another pretextual and retaliatory action,” vowing to fight it. The university insisted it is committed to ensuring that members of Jewish and Israeli communities are embraced and respected, and can thrive on campus, charging that its efforts to do so reflect the opposite of “deliberate indifference.”

The lawsuit comes after negotiations appear to have bogged down in the months-long battle with the Trump administration that has tested the boundaries of the government’s authority over America’s universities. What began as an investigation into campus antisemitism escalated into an all-out feud as the Trump administration slashed more than $2.6 billion in research funding, ended federal contracts and attempted to block Harvard from hosting international students.

In a pair of lawsuits filed by the university, Harvard has said it’s being unfairly penalized for refusing to adopt the administration’s views. A federal judge agreed in December, reversing the funding cuts and calling the antisemitism argument a “smokescreen.”

Even so, Harvard and the Trump administration have held some negotiations, and the two sides have reportedly been close to reaching an agreement on multiple occasions. Last year, the administration and the university were reportedly approaching a deal that would have required Harvard to pay $500 million to regain access to federal funding and to end the investigations. Almost a year later, Trump upped that figure to $1 billion, saying that Harvard has been “behaving very badly.”

At the same time, the administration was taking steps in a civil rights investigation that had the potential to jeopardize all of Harvard’s federal funding, including federal student aid.

In June, the Trump administration said a civil rights investigation had led to a formal finding that Harvard tolerated antisemitism.

In a letter sent to Harvard, a federal task force said its investigation had found the university was a “willful participant” in antisemitic harassment of Jewish students and faculty. The task force threatened to refer the case to the Justice Department to file a civil rights lawsuit “as soon as possible,” unless Harvard came into compliance.

Harvard responded that it strongly disagreed with the government’s findings and was committed to fighting bias.

“Antisemitism is a serious problem and no matter the context, it is unacceptable,” the university said in a statement. “Harvard has taken substantive, proactive steps to address the root causes of antisemitism in its community.”

Since he took office, Trump has targeted elite universities he believes are overrun by left-wing ideology and antisemitism, which has spiked on university campuses across the US since the Hamas-led October 7, 2023, onslaught against Israel started the war in Gaza. His administration has frozen billions of dollars in research grants, which colleges have come to rely on for scientific and medical research.

Several universities have reached agreements with the White House to restore funding. Some deals have included direct payments to the government, including $200 million from Columbia University. Brown University agreed to pay $50 million toward state workforce development groups.

Times of Israel staff contributed to this report.

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