The Ivy League university, however, denounced the allegations, describing them as retaliatory action that threatens its community.
The Trump administration is ending Harvard University's ability to enroll international students by revoking its Student and Exchange Visitor Programme certification.
The Department of Homeland Security (DHS), on Thursday, attributed this to the university's refusal to comply with its requests for the behavioural records of student visa holders.
The Homeland Security Secretary, Kristi Neom, in a post on X, also accused the school of fostering an unsafe campus environment, hostility to Jewish students, support for Hamas, and what she described as racist DEI initiatives.
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"Let this serve as a warning to all universities and academic institutions across the country. This administration is holding Harvard accountable for fostering violence, antisemitism, and coordinating with the Chinese Communist Party on its campus," she said.
"It is a privilege, not a right, for universities to enrol foreign students and benefit from their higher tuition payments to help pad their multibillion-dollar endowments. Harvard had plenty of opportunities to do the right thing. It refused.
"They have lost their 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."
This new policy could affect thousands of international students, some of whom are Nigerians, currently studying at the institution.
Nigerians have consistently been among the international student community at Harvard, pursuing degrees across various disciplines. Nigerians make up nearly one-quarter of the black students at the Harvard Business School.
According to Harvard University's One World programme, the Ivy League institution has so far enrolled about 6,793 international students.
This represents about 27.2 per cent of its total student body. It would also affect the admission of students for the coming academic year.
Repeated attacks
This policy is the latest attempt to pressure the university and other elite universities in the US as part of the Trump administration's broader effort to change race-conscious admissions policies and challenge what it considers to be liberal bias in academia.
Harvard University, in the past months, has been targeted by the president for refusing many of the changes to admission, curriculum and hiring practices that his administration has pushed.
The school has faced threats, growing scrutiny from federal officials and even aid cuts. Last month, the US Department of Education froze $2.3 billion in federal funds to the university.
The department, in March, launched an investigation into the university and 51 other schools, accusing them of racial preference and stereotypes in education programmes.
In the latest development, the administration said Harvard may no longer enrol foreign students in the 2025-2026 school year.
It also stated that existing foreign students must transfer or lose their legal status to reside in the US before the next academic year begins.
The Homeland Security Secretary described this as a consequence of Harvard's refusal to comply with "simple reporting requirements."
"As a result of your brazen refusal to comply with multiple requests to provide the Department of Homeland Security pertinent information while perpetuating an unsafe campus environment that is hostile to Jewish students, promotes pro-Hamas rhetoric, and employs racist 'diversity, equity, and inclusion' policies, you have lost this privilege," she wrote in a letter to University.
Mrs Noem, however, offered the institution 72 hours to provide the information requested for an opportunity to regain its visa programme for the next school year.
Harvard's response
Responding to this, the Ivy League university denounced the allegations made against it and described the directive as retaliatory action that threatens its community.
In a statement issued shortly after the announcement, it reaffirmed its commitment to campus safety, academic freedom, and support for all students, regardless of background or nationality.
"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."
"We are working quickly to provide guidance and support to members of our community. This retaliatory action threatens serious harm to the Harvard community and our country, and undermines Harvard's academic and research mission."
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Last month, Harvard introduced a temporary policy change permitting international students to hold admission offers from both Harvard and a foreign university as a contingency plan.
Typically, admitted students are required to commit solely to Harvard by 1 May.
At least twelve Harvard students have had their permission to study in the United States rescinded due to their involvement in campus protests.
PREMIUM TIMES also reported that about 600 international students in over 90 colleges and universities have had their visas revoked or their legal status terminated in the last months.
Earlier in the week, the US Secretary of State, Marco Rubio, said the State Department had likely revoked thousands of student visas across the country and was open to revoking more.
"We're going to continue to revoke the visas of people who are here as guests and are disrupting our higher education facilities.
"A visa is a privilege, not a right," he said to Congress on Tuesday.
