Thousands of Harvard students in crimson-fringed gowns celebrated their graduation on Thursday, as a federal judge said she would temporarily block Donald Trump's bid to bar the prestigious university from enrolling international scholars.

Trump has made Harvard the central target of his campaign against elite US universities, which he has threatened with funding freezes and action against their foreign students over what he says is liberal bias and anti-Semitism.

A federal judge in Boston said she would issue an order that "gives some protection" to international students while courts consider the legality of Trump's effort to block Harvard from enrolling foreign students.

"We want to make sure there's no more shenanigans between now and then," said Harvard's lawyer Ian Gershengorn.

"Our students are terrified and we're [already] having people transfer" to other universities, he said.

In an eleventh-hour filing ahead of the hearing, the Trump administration issued a formal notice of intent to withdraw Harvard's ability to enrol foreign students – kickstarting the process.

The filing gave Harvard 30 days to produce evidence showing why it should not be blocked from hosting and enrolling foreign students.

Judge Allison Burroughs had already temporarily paused the policy affecting some 27 percent of Harvard's student body, extending that pause on Thursday.

She said she would seek to determine "whether they were terminated for a retaliatory motive."

A law professor present in the packed court said the Trump administration was prolonging the suffering of international students. (AFP)