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The Trump administration has declared that Harvard University is in “severe violation” of civil rights law and must “promptly” address the issue or risk losing all federal funding.

A letter from the health department’s office for civil rights, obtained by the Financial Times, states that Harvard has violated the Civil Rights Act’s ban on discrimination based on race, color, and national origin.

This decision represents a new level of conflict between the prestigious university and the Trump administration, even after the president had indicated earlier this month that a resolution might be within reach.

Harvard has launched lawsuits challenging the administration’s moves against it, which include efforts to halt federal funding and prevent the university from enrolling international students.

The letter, sent on Monday, comes as the administration piles pressure on the US’s higher-education institutions, including the University of Virginia, whose president James Ryan resigned last week after coming under attack by the administration.

The administration claimed that Harvard had been “in some cases deliberately indifferent, and in others has been a wilful participant in antisemitic harassment of Jewish students, faculty, and staff”.

It added: “Harvard’s commitment to racial hierarchies — where individuals are sorted and judged according to their membership in an oppressed group identity and not individual merit — has enabled antisemitism to fester on Harvard’s campus and has led a once great institution to humiliation, offering remedial math and forcing Jewish students to hide their identities and ancestral stories.”

Many academics and civil rights groups including some Jewish organisations have criticised the Trump administration’s attacks on US universities as a threat to freedom of speech and academic freedom.

US university leaders recently signed a statement saying they “must oppose undue government intrusion” into the academy.”

Alan Garber, Harvard’s president, in April made public reports it had commissioned on antisemitic and anti-Muslim bias, which highlighted concerns and made recommendations for reform.

He said at the time that the university was redoubling its efforts and that “Harvard cannot — and will not — abide bigotry. We will continue to provide for the safety and security of all members of our community and safeguard their freedom from harassment.”

Harvard did not immediately respond to a request to comment on the latest White House action.