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Harvard University on Monday sued the Trump administration to block its “unlawful” efforts to freeze more than $3bn in federal funding and increase government oversight of the venerable institution. 

In a statement, Harvard’s president, Alan Garber, warned the government’s “sweeping and intrusive demands . . . would impose unprecedented and improper control over the University” with “stark real-life consequences for patients, students, faculty, staff, researchers, and the standing of American higher education in the world”.

He added: “We stand for the truth that colleges and universities across the country can embrace and honour their legal obligations and best fulfil their essential role in society without improper government intrusion.”

The government has accused Harvard of failing to combat antisemitism on campus. After freezing $2.2bn in federal funding earlier this month it is also looking to block future grants worth hundreds of millions of dollars from Harvard and four other elite US universities.

In an email leaked to the journal Nature and published on X on Monday, a senior official from the National Institutes of Health instructed colleagues to “hold off on making awards” to Harvard, Brown, Columbia, Cornell and Northwestern universities — and to provide no reason for cuts. Last year’s grants to these institutions totalled $1.7bn.

The Trump administration has also threatened to revoke Harvard’s tax- exempt status after the university leadership rejected demands for tight government controls over its academic freedom.

Separately, letters leaked to The College Fix publication last week showed the Office of Civil Rights of the US Department of Health and Human Services demanded Harvard provide copies of all its findings or draft reports on combating antisemitism and anti-Israeli bias, as well as others on anti-Muslim, anti-Arab and anti-Palestinian bias. 

Seven universities have been singled out for targeted government cuts since March. Michael Kotlikoff, president of Cornell, said in an email to his university on Monday that he had received no official government communication confirming a $1bn freeze announced in early April.

But he added Cornell researchers had received a series of “stop work” orders from government funders, and said the university was “responding forcefully”. “That includes legal, strategic, and policy-level engagement to reverse these actions and prevent further disruption,” he added.

Separately, the government has in recent weeks stepped up detentions of pro-Palestinian student demonstrators around the country, revoking hundreds of visas of international students. Last week it demanded that Harvard provide detailed records of its “foreign student visa holders’ illegal and violent activities” or lose its eligibility to receive foreign students.

Harvard responded that it would “not surrender its independence or relinquish its constitutional rights”. “We will continue to comply with the law and expect the administration to do the same,” Garber said in a statement.

The university has created committees to investigate antisemitism and released their preliminary recommendations last summer. Garber said on Monday that this and a separate report on Muslim, anti-Arab, and anti-Palestinian bias would be published “soon”.

The Wall Street Journal reported that the government’s antisemitism task force had been angered by Harvard’s decision to release its letter and was planning further freezes of $1bn.

The decision by Harvard to defy the government’s demands — in contrast to Columbia University’s concessions to the administration’s order for an overhaul of governance and student discipline — has sparked a surge in donations by alumni, with several thousand contributions reported by the Crimson newspaper last week.

Faculty members, students and alumni at other universities have also stepped up their demands for greater co-ordination in resisting the Trump administration’s attacks on higher education institutions.

Claire Shipman, the acting president of Columbia, said in a statement: “Though we seek to continue constructive dialogue with the government, we would reject any agreement that would require us to relinquish our independence and autonomy as an educational institution.”

Harvard is in a better position than most universities to withstand cuts in government funding; its $53bn endowment is the largest of any higher education institution in the US. 

Several universities, including Harvard, have turned to the bond markets to generate short-term cash, providing them with liquidity to help bridge the short-term drop in funding and potential upcoming legal battles. Many have also implemented job freezes and cost-cutting measures.