The lawsuit, filed in federal court in Massachusetts, is another salvo in a protracted battle between the administration of President Donald Trump and the elite university.

“The United States cannot and will not tolerate these failures,” the Justice Department wrote in the lawsuit. It asked the court to compel Harvard to comply with federal civil rights law and to help it “recover billions of dollars of taxpayer subsidies awarded to a discriminatory institution.”

The lawsuit also asks a judge to require that Harvard call police to arrest protesters blocking parts of campus and to appoint an “independent outside monitor,” approved by the government, to ensure it complies with court orders.

Harvard did not immediately respond to a request for comment.

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.”

Ted Mitchell, president of the American Council on Education, a major association of colleges and universities, accused the administration of launching a “full scale, multi-pronged” attack on Harvard. Friday’s lawsuit, he said, is just the latest attempt to pressure Harvard to agree to changes favored by the administration.

“When bullies pound on the table and don’t get they want, they pound again,” Mitchell said.

The Trump administration began investigating allegations of discrimination against Harvard’s Jewish and Israeli students less than two weeks after the president took office. The allegations focus on Harvard’s actions during and after pro-Palestinian demonstrations during the Israel-Hamas war.

Officials concluded Harvard did not adequately address concerns raised about antisemitism that drove some students to conceal their religious skullcaps and avoid classes. During protests of the war, Trump officials said, Harvard permitted students to demonstrate against Israel’s actions in the school library and allowed a pro-Palestinian encampment to remain on campus for 20 days, “in violation of university policy.”

In its lawsuit Friday, the Justice Department also accused Harvard of failing to discipline staff or students who protested or tacitly endorsed the demonstrations, such as by canceling or dismissing classes that conflicted with protests.

“Harvard University has failed to protect its Jewish students from harassment and has allowed discrimination to wreak havoc on its campus,” White House press secretary Liz Huston said Friday on X. “President Trump is committed to ensuring every student can pursue their academic goals in a safe environment.”

Despite their bitter dispute, 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.

In June, the Trump administration made 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.

When colleges are found in violation of federal civil rights law, they almost always reach compliance through voluntary agreements. When the government determines a resolution can’t be negotiated, it can try to sever federal funding through an administrative process or, as the Trump administration has done, by referring the case to the Justice Department through litigation.

Such an impasse has been extraordinarily rare in recent decades.

Last summer, Harvard responded that it strongly disagreed with the government’s investigative finding 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.”

In a letter last spring, Harvard President Alan M. Garber told government officials that the school had formed a task force to combat antisemitism, which released a detailed report of what unfolded on campus after Hamas militants stormed Israel on Oct. 7, 2023, killing around 1,200 people and abducting 251 others. Israel retaliated with an offensive that killed tens of thousands of Palestinians and displaced around 90% of Gaza’s population — prompting pro-Palestinian demonstrations at colleges around the country.

After the demonstrations at Harvard, Garber said the university had hired a new provost and new deans and that it had reformed its discipline policies to make them “more consistent, fair and effective.”

Since he took office, Trump has targeted elite universities he believes are overrun by left-wing ideology and antisemitism. 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.

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AP Education Writer Collin Binkley contributed to this report.

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