Harvard called the move "unlawful" in a statement.
The Trump administration has moved to end Harvard's ability to enrol international students, escalating a standoff with America's oldest university.
Homeland Security Secretary Kristi Noem wrote on X that the administration had revoked Harvard's "Student and Exchange Visitor Program certification as a result of their failure to adhere to the law."
"Let this serve as a warning to all universities and academic institutions across the country," she wrote on Thursday.
Harvard called the move "unlawful" in a statement.
"We are fully committed to maintaining Harvard's ability to host our international students and scholars, who hail from more than 140 countries and enrich the University – and this nation – immeasurably," the university responded.
The Trump administration's decisions could affect thousands of international students who study at the university. Over 6,700 international students were enrolled at the institution last academic year, university data shows, making up 27% of its student body.
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