Trump is seeking to bring the universities to heel with claims their international students pose a national security threat, and that they ignored anti-Semitism on campus and perpetuate liberal bias.
A proclamation issued by the White House late Wednesday declared that the entrance of international students to begin a course at Harvard would be "suspended and limited" for six months and that existing overseas enrollees could have their visas terminated.
"Harvard's conduct has rendered it an unsuitable destination for foreign students and researchers," the order said.
Karl Molden, a Harvard government and classics student from Austria, said: "I'm trembling. This is outrageous."
"He is abusing his executive power to harm Harvard as much as he can," Molden told AFP.
"My god!" said another international student at Harvard, who declined to be identified for fear of retribution.
"This is such a disgrace."
China's foreign ministry vowed on Thursday to "resolutely safeguard the legitimate rights and interests of its overseas students."
"China has always opposed the politicization of educational cooperation," ministry spokesman Lin Jian said, adding that the measure would "harm America's image and international credibility."
US Secretary of State Marco Rubio promised last week to "aggressively revoke visas" for Chinese students, a move condemned by Beijing.
- 'Retaliatory' -
Wednesday's announcement followed the Trump administration's earlier efforts to terminate Harvard's right to enroll and host foreign students were stalled by a judge.
The government already cut around $3.2 billion of federal grants and contracts benefiting Harvard and pledged to exclude the Cambridge, Massachusetts, institution from any future federal funding.
Harvard has been at the forefront of Trump's campaign against top universities after it defied his calls to submit to oversight of its curriculum, staffing, student recruitment and "viewpoint diversity."
Trump has also singled out international students at Harvard, who accounted for 27 percent of total enrollment in the 2024-2025 academic year and are a major source of income.
"This is yet another illegal retaliatory step taken by the Administration in violation of Harvard's First Amendment rights," a university spokesman said.
"Harvard will continue to protect its international students."
Trump's education secretary had also threatened on Wednesday to strip Columbia University of its accreditation.
The Republican has targeted the New York Ivy League institution for allegedly ignoring harassment of Jewish students, throwing all of its federal funding into doubt.
Unlike Harvard, several top institutions -- including Columbia -- have already bowed to far-reaching demands from the Trump administration, which claims that the educational elite is too left-wing.
- 'Combating anti-Semitism' -
Wednesday's official action suggested it was not enough for Trump.
"Columbia University looked the other way as Jewish students faced harassment," US Education Secretary Linda McMahon said on social media platform X.
She accused the school of breaking rules prohibiting recipients of federal funding from discriminating on the basis of race, color, or national origin.
"After Hamas' October 7, 2023, terror attack on Israel, Columbia University's leadership acted with deliberate indifference towards the harassment of Jewish students on its campus," McMahon said in a statement.
"This is not only immoral, but also unlawful."
The US Education Department said in the statement its civil rights office had contacted Columbia's accreditation body about the alleged violation.
Withdrawing Columbia's accreditation would see it lose access to all federal funding, a very significant proportion of the university's income.
Students would also not be able to receive federal grants and tuition loans.
Critics accuse the Trump administration of using allegations of anti-Semitism to target educational elites and bring universities to their knees.
The administration has already put $400 million of Columbia's funding under review, prompting the university to announce in March a package of concessions to the government around defining anti-Semitism, policing protests and conducting oversight for specific academic departments.
A Columbia spokesperson said after Wednesday's announcement the university was "aware of the concerns" raised by the government.
"We take this issue seriously and are continuing to work with the federal government to address it," the spokesperson said.
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