The two universities filed a lawsuit in federal court in Boston asking for an emergency temporary restraining order on the new directive issued by the government on Monday.
"We will pursue this case vigorously so that our international students - and international students at institutions across the country - can continue their studies without the threat of deportation," Harvard President Lawrence Bacow wrote in a statement addressed to the Harvard community.
The lawsuit filed by Harvard and MIT, two of the most elite US universities, is the first to challenge the order that could force tens of thousands of foreign students to leave the country if their schools switch fully to remote learning.
Harvard had announced it would hold all classes online in the coming fall term.
The US Department of Justice did not immediately respond to a request for comment on the lawsuit.
US President Donald Trump is pushing schools across the country to re-open in the fall.
The Trump administration announcement blindsided academic institutions grappling with the logistical challenges of safely resuming classes as the coronavirus pandemic continues unabated around the world, and surges in the United States, especially among young people.
There are more than a million foreign students at US colleges and universities, and many schools depend on revenue from foreign students, who often pay full tuition.
The US Immigration and Customs Enforcement (ICE) agency rule said most students on F-1 and M-1 visas could stay if their programs were in person or offered a mix of online and in-person instruction.
In the wake of the announcement, students, professors, and universities were scrambling to figure out exactly who would be affected by the rule and come up with ways to comply without having to leave the country. On Twitter, professors across the country offered to teach outdoor in-person independent study courses for affected students.
The ICE policy change marked an unexpected reversal of exceptions to the rules limiting online learning for foreign students when colleges and universities in March rushed to shutter campuses and move to virtual classes as the pandemic forced lockdowns.
ICE "proceeded without any indication of having considered the health of students, faculty, university staff, or communities," the complaint said.
The suit alleges the government skirted the proper rulemaking process and is asking the court to strike it down.
Judge Allison Burroughs, appointed by former President Barack Obama, is assigned to hear the case. In 2017, she ordered a halt to Trump's travel ban on several Muslim-majority countries, a policy that was eventually upheld by the US Supreme Court.
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