Mahmoud Khalil, a graduate student at Columbia until December, was inside his university-owned apartment on Saturday night when several Immigration and Customs Enforcement agents entered and took him into custody, his lawyer Amy Greer, told The Associated Press.
US President Donald Trump labelled Khalil "a radical foreign pro-Hamas student" in a post on his online platform Truth Social on Monday.
Trump said he would deport him from the US along with others involved in "pro-terrorist, anti-Semitic and anti-American activity".
In a message shared on X Sunday evening, Secretary of State Marco Rubio said the administration "will be revoking the visas and/or green cards of Hamas supporters in America so they can be deported".
Greer says Khalil has an unlimited US residence permit, a so-called green card and revoking such status is usually a lengthy process.
Khalil intends to take legal action against his deportation, Greer said.
The New York Times reported that the Palestinian is married to a woman who is a US citizen and is eight months pregnant.
A court had initially blocked Khalil's deportation to allow time for a ruling, according to media reports.
Protests against Israel's actions in the Gaza war have taken place at New York's elite Columbia University and many other universities in the US.
Camps were set up, buildings were occupied and Khalil played a prominent role as a speaker at the demonstrations in New York.
Columbia is being targeted by the Trump administration, which believes the demonstrators there sympathise with Palestinian Islamist Hamas militants in Gaza and that Jewish students on campus are not sufficiently protected.
The university recently had $US400 million ($A637 million) in funding cancelled.
with AP
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