US Immigration and Customs Enforcement said people could face deportation unless they change to an institution with in-person tuition.
US universities are considering online teaching in the new academic year due to coronavirus.
The Student and Exchange Visitor Programme, which is operated by ICE, introduced a temporary exemption to allow students whose courses had moved online for the spring and summer semesters to remain in the US. The exemption will not be extended and affects students who are in the US on F-1 and M-1 visas.
9% of US universities are planning to teach all their classes online in the autumn.
The president of Harvard University, Larry Bacow, said in a statement:
"We are deeply concerned that the guidance issued today by US Immigration and Customs Enforcement imposes a blunt, one-size-fits-all approach to a complex problem, giving international students, particularly those in online programmes, few options beyond leaving the country or transferring schools."
"Kicking international students out of the US during a global pandemic because their colleges are moving classes online for physical distancing hurts students," said Democratic Senator Elizabeth Warren. "It's senseless, cruel, and xenophobic."
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