A court hearing in the case is scheduled for Wednesday.
Trump publicly criticized Khalil and said additional arrests would follow. Khalil, who had been moved to a federal immigration detention center in Louisiana, is awaiting deportation proceedings, his lawyers and a US detainee database confirmed.
His arrest by Department of Homeland Security (DHS) agents has drawn widespread condemnation from protesters in New York, the state attorney general, and the American Civil Liberties Union, who have called it an attack on free speech.
In lower Manhattan, police clashed briefly with hundreds of demonstrators, and at least one person was detained, a Reuters witness reported.
Khalil, a legal permanent US resident who was arrested on Saturday, has been a prominent figure in Columbia’s pro-Palestinian student movement, which fueled campus demonstrations across the US and abroad last year. Trump labeled him a "Radical Foreign Pro-Hamas Student" on social media.
On Monday, US District Court Judge Jesse Furman ordered a stay on Khalil’s deportation "unless and until the Court orders otherwise."
Khalil’s lawyers urged Furman to return him to New York, arguing that the government was trying to limit his access to legal counsel by detaining him far from the city.
Trump, in a social media post, said Khalil’s case was "the first arrest of many to come." While the administration has not stated that Khalil is charged with any crime, Trump claimed his presence in the US was "contrary to national and foreign policy interests."
The US Education Department on Monday warned 60 universities, including Columbia, Harvard, Yale, and several University of California schools, that they risk losing federal funding unless they address alleged antisemitism on campus.
Even before Khalil’s arrest, Columbia students reported seeing federal immigration agents near student housing. The Trump administration announced Friday that it was revoking $400 million in federal grants and contracts awarded to Columbia, citing antisemitic harassment on and around campus.
According to the Student Workers of Columbia labor union, federal agents have also sought to detain at least one other international student. DHS and Immigration and Customs Enforcement (ICE) declined to comment, and Reuters was unable to verify the union's claim independently.
A State Department spokesperson said visa records are confidential under US law and could not be discussed.
‘Chilling Effect’
On Saturday evening, DHS agents arrested Khalil in front of his wife, a US citizen who is eight months pregnant, telling him his student visa had been revoked, said Amy Greer, his attorney.
When Khalil’s wife presented his green card, agents allegedly told her it had also been revoked and threatened to arrest her if she did not leave the lobby, Greer said. Khalil was then handcuffed.
Hours before his arrest, Khalil told Reuters he feared the government was targeting him. He and other activists argue that their criticism of Israel and US policy is wrongly equated with antisemitism, noting that Jewish students have been among the protest organizers.
Jewish faculty at Columbia held a rally Monday in support of Khalil, carrying signs reading, "Jews say no to deportations."
"There is a chill in the air. It's a chill of fear and despair," said Marianne Hirsch, a Columbia professor of English and comparative literature, whose parents were Holocaust survivors.
While Trump and his administration have cited antisemitism concerns, critics have accused him and his allies of enabling it.
Following a 2017 white nationalist rally in Charlottesville, Virginia—where some protesters chanted "Jews will not replace us"—Trump said there were "fine people on both sides."
Trump, who denies allegations of antisemitism, also faced criticism in 2022 for dining with white supremacist Nick Fuentes.