Mohsen Mahdawi, an organizer of the pro-Palestinian movement at Columbia University, was freed from federal custody on Wednesday as immigration officials seek to rescind his green card as part of a widening crackdown against student protesters.

In ruling to release Mr. Mahdawi on bail, Judge Geoffrey W. Crawford of Federal District Court in Vermont found on Wednesday that he did not pose a danger to the public and that he was not a flight risk. The judge drew parallels between the current political climate and McCarthyism, saying it was “not our proudest moment.”

The immigration case against Mr. Mahdawi will continue, his lawyers said, but he will now be able to fight it from outside a detention facility.

Mr. Mahdawi’s release is a defeat for the Trump administration, although other students remain in detention as part of the government’s campaign.

The secretary of state, Marco Rubio, has argued that protesters like Mr. Mahdawi have spread antisemitism, while demonstrators say criticism of Israel’s actions in Gaza is not antisemitic.

Mr. Rubio has said that immigration authorities have the right to eject even legal residents from the country for protest activities that the government says harm America’s foreign policy interests.