Alan M. Garber, the president of Harvard, said in a message to the university community Monday that the Trump administration’s actions are unlawful and beyond the government’s authority.

Although some members of the administration have said their letter of demands sent this month was issued by mistake, Garber said, other statements and actions suggest otherwise: In addition to a freeze of $2.2 billion in federal funding, the government has considered taking steps to freeze an additional $1 billion in grants, initiated numerous investigations of Harvard’s operations, threatened the education of international students and said that it is considering a revocation of Harvard’s tax-exempt status.

Garber noted that the government has cited the university’s response to antisemitism as a justification for its actions.

“As a Jew and as an American, I know very well that there are valid concerns about rising antisemitism,” he said. And to address those concerns effectively “requires understanding, intention, and vigilance. Harvard takes that work seriously. We will continue to fight hate with the urgency it demands as we fully comply with our obligations under the law. That is not only our legal responsibility. It is our moral imperative.”

The Ivy League university is accusing the Trump administration of violating its First Amendment rights, federal administrative procedures and regulations for taking action against institutions. Harvard also claims that while Trump administration officials have accused the school of violating Title VI, a federal law that says any school found to violate civil rights is not eligible for federal funding, they failed to follow the procedures set out in the law.

The president and fellows of Harvard College filed the sweeping complaint against the departments of Health and Human Services, Education, Energy, and Defense, the General Services Administration, the National Institutes of Health, NASA, and the leaders of those agencies.

According to the complaint, the “fatal procedural shortcomings are compounded by the arbitrary and capricious nature” of the decision. Before the funding freeze, the government had threatened to terminate nearly $9 billion in federal funding, not just to Harvard, but also to affiliated Boston hospitals and independent corporate entities not under Harvard’s control.

Harrison Fields, a spokesperson for the White House, responded to the lawsuit by saying, “The gravy train of federal assistance to institutions like Harvard, which enrich their grossly overpaid bureaucrats with tax dollars from struggling American families is coming to an end. Taxpayer funds are a privilege, and Harvard fails to meet the basic conditions required to access that privilege.”

Kermit Roosevelt, a professor at the University of Pennsylvania Carey Law School, said Harvard has a solid case, especially the claims alleging the government violated Title VI and the Administrative Procedure Act.

“It looks as though the administration is just sort of doing what it wants to without real concern for what the law is,” said Roosevelt, an expert on constitutional law. He said a win for Harvard could embolden other universities to fight back against the Trump administration, but a loss in this case could mean the “end of the resistance.”

Jason Rubenstein, the executive director of Harvard Hillel, said that the school is in the midst of a long — and long-overdue — reckoning with antisemitism, and that Garber has taken important steps to address the problem. Methodical federal civil rights oversight could play a constructive role in that reform, he said. “But the government’s current, fast-paced assault against Harvard – shuttering apolitical, life-saving research; targeting the university’s tax-exempt status; and threatening all student visas … is neither deliberate nor methodical, and its disregard for the necessities of negotiation and due process threatens the bulwarks of institutional independence and the rule of law that undergird our shared freedoms.”

The Trump administration had initially announced a review of nearly $9 billion in federal funding to Harvard as it cracked down on colleges that it claims are overrun with antisemitism and leftist ideology. As part of the review, officials demanded in an April 11 letter that the university upend its hiring, admissions and governance and submit to years-long federal oversight of multiple aspects of its operations.

When Harvard made clear last week that the university would not comply, the administration responded forcefully by freezing $2.2 billion in funding. Within days, it also sought to revoke the school’s tax-exempt status and threatened to bar the institution from enrolling international students if certain student records were not turned over.

The administration’s actions against universities have touched off protests nationally with a coordinated “day of action” Thursday at scores of campuses. Thousands of professors signed letters inspired by one written to the Harvard Corp. urging the school’s leaders to refuse to acquiesce to unlawful demands and to mount a coordinated response with other schools and alumni. Other prominent university presidents spoke out in support of Harvard’s stance this week, as well as political leaders such as former president Barack Obama, a graduate of its law school.

On Monday, Harvard’s chapter of the American Association of University Professors, which filed a lawsuit earlier this month to block the Trump administration’s cuts, praised the university for taking legal action.

“It is high time for leading civil society institutions like Harvard to refuse and resist this federal government overreach and abuse,” said Kirsten Weld, a history professor at Harvard and president of the AAUP Harvard faculty chapter.

The administration’s approach, which it deems necessary to combat campus antisemitism, has some prominent advocates. Kenneth L. Marcus, founder and chief executive of the Brandeis Center for Human Rights Under Law, a Jewish civil rights nonprofit, said before the lawsuit was filed that such a “whole-of-government response” was long overdue and appropriate given the breadth of the problem.

“This is by far the most sweeping and comprehensive approach we’ve seen to antisemitism in this country,” said Marcus, who headed the Education Department’s Office for Civil Rights during the first Trump administration and faulted the Biden administration for not taking a more aggressive stance after campus protests began over Israel’s military operation in Gaza.

Harvard leaders said the government’s directives — conveyed in the wide-ranging five-page letter — were unlawful and unconstitutional. The steps ordered, they warned, would be critically damaging to a generations-long partnership between the federal government and universities that had powered scientific advances.

“No government — regardless of which party is in power — should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue,” Garber told the campus community last week.

In announcing the lawsuit Monday, Garber listed research jeopardized by the funding freeze, including efforts to understand how cancer spreads, to predict the spread of infectious-disease outbreaks, and to reduce the risk of multiple sclerosis, Alzheimer’s disease and Parkinson’s disease.

“The consequences of the government’s overreach will be severe and long-lasting,” Garber wrote.

The administration’s multiagency Joint Task Force to Combat Anti-Semitism said last week that the school’s position reflected “the troubling entitlement mindset that is endemic in our nation’s most prestigious universities and colleges — that federal investment does not come with the responsibility to uphold civil rights laws.”

Though Harvard’s $53 billion endowment makes it the wealthiest university in the country, much of that money is restricted by donors and the terms of their gifts. The same night the funding freeze was announced, the first stop-work orders on major research projects were already hitting the school.

The next day, Trump posted on social media: “Perhaps Harvard should lose its Tax Exempt Status and be Taxed as a Political Entity if it keeps pushing political, ideological, and terrorist inspired/supporting ‘Sickness?’ Remember, Tax Exempt Status is totally contingent on acting in the PUBLIC INTEREST!”

“It’s just unfathomable,” said Lily Batchelder, a professor of law at New York University and former assistant secretary of tax policy for the Treasury Department. “Congress has repeatedly enacted laws that make it a crime for the president or any political appointees to help the White House to directly or indirectly interfere in IRS audits or investigations of taxpayers, and the president has done just this by tweeting that he wants them to do so.”

Even without political influence, she said it would be extremely rare for the IRS to revoke an organization’s tax-exempt status and would only happen after years of investigation and back-and-forth.

“This is a really profound undermining of the law,” Batchelder said, adding that all Americans should be worried about the ramifications for nonprofits they care about, whether a church congregation or community group.

A White House spokesperson said last week that investigations into an array of institutions began before Trump posted on Truth Social and that any forthcoming actions would be conducted independently of the president.

Jason Newton, a spokesperson for Harvard, said there is no legal basis to rescind the school’s tax-exempt status. The government, he noted, has long exempted universities from taxes to support their educational mission: “The tax exemption means that more of every dollar can go toward scholarships for students, lifesaving and life-enhancing medical research, and technological advancements that drive economic growth.”

Homeland Security Secretary Kristi L. Noem also has weighed in, demanding that Harvard supply records on international students alleged to have engaged in “illegal and violent activities” or face losing its certification to enroll foreign students. According to the Institute of International Education, Harvard had about 7,800 international students enrolled last academic year.

Other schools — starting with Columbia University, but including Princeton, Cornell, Brown and Northwestern universities and the University of Pennsylvania — are facing funding threats too.

Harvard’s stand drew support from several of those institutions’ leaders last week, though other college presidents continued to remain silent publicly. Unions representing faculty members had already brought lawsuits challenging the Trump administration’s actions at Columbia and Harvard.

Columbia’s acting president, Claire Shipman, said in a statement last week to her university community that she had read “with great interest” Harvard’s response to the government’s demands. Columbia has seen hundreds of research grants terminated, and funding hasn’t been restored despite its efforts to negotiate with the government. Those discussions are continuing, Shipman wrote, but she made clear that there were lines the university would not cross.

Columbia would reject any agreement in which the government dictates what the school teaches, researches or whom it hires, she wrote. Overly prescriptive “requests about our governance, how we conduct our presidential search process, and how specifically to address viewpoint diversity issues are not subject to negotiation,” she noted, and the school “would reject any agreement that would require us to relinquish our independence and autonomy as an educational institution.”

Princeton President Christopher Eisgruber last week linked to Garber’s letter in a post on LinkedIn and wrote, “Princeton stands with Harvard. I encourage everyone to read President Alan Garber’s powerful letter in full.”

Eisgruber had previously spoken out, writing in the Atlantic in March that the Trump administration’s attack on Columbia was “the greatest threat to American universities since the Red Scare.” After Princeton was targeted with cuts, he told the campus community that the school would “vigorously defend” academic freedom.

And in a message to their community last week, Stanford University President Jonathan Levin and Provost Jenny Martinez said the Supreme Court had long ago recognized the freedoms of universities under the First Amendment as the ability to determine who gets to teach, what is taught, how subjects are taught and who is admitted to study.

Universities need to address legitimate criticisms with humility, they wrote — but the way to bring about constructive change is not by destroying the nation’s capacity for scientific research or through the government taking control of a private institution. “Harvard’s objections to the letter it received are rooted in the American tradition of liberty,” they wrote, “a tradition essential to our country’s universities, and worth defending.”

On Tuesday, a group of more than 100 college presidents and other higher education leaders publicly spoke out: In a collective statement from the American Association of Colleges and Universities, the leaders said they reject the “coercive use of public research funding.” They said they are open to constructive reform and do not oppose legitimate government oversight, but “we must oppose undue government intrusion in the lives of those who learn, live, and work on our campuses.”