A judge on Wednesday is expected to scrutinize the constitutional issues at play in the case of Mahmoud Khalil, a recent Columbia University graduate and permanent legal resident who was arrested over the weekend and taken to a Louisiana detention center.

The judge, Jesse Furman, has ordered the government not to remove Mr. Khalil from the United States while his case is pending.

Mr. Khalil, who has Palestinian heritage, was a leader of demonstrations against Israel’s war in Gaza, which rocked Columbia’s campus last year. Mr. Khalil has not been accused of any crime and his swift arrest and transfer have raised alarms about free speech protections as President Trump promises to crack down on protests at colleges.

Judge Furman has the power to order Mr. Khalil’s release, but it is unclear whether he might do so as early as the conference, on Wednesday morning at 11:30. The conference, however, could provide more information about the circumstances that led to the arrest and the government’s justification for Mr. Khalil’s continuing detention.

The future of Mr. Khalil’s immigration status will be decided in a separate process. That matter will be presided over by an immigration judge, who could determine whether to revoke Mr. Khalil’s green card.

Lawyers for Mr. Khalil have asked Judge Furman to return their client to New York and reunite him with his wife, an American citizen who is expected to give birth next month. At the Wednesday conference, the lawyers are expected to argue that his detention is a clear-cut retaliation for constitutionally protected speech on behalf of Palestinian people.

“Because Mahmoud has been so prominent, active and outspoken in support of Palestinian rights, he’s been marked as a target,” said one of his lawyers, Ramzi Kassem, a co-director of CLEAR, a legal clinic at the City University of New York. “What’s being done to him is unconstitutional, it is unlawful, and we intend to do everything in our power to ensure the Trump administration will not get away with it in court.”

The government will initially be represented by lawyers from the U.S. attorney’s office in Manhattan. A spokesman for the office declined to comment on how it might address the questions raised by Mr. Khalil’s arrest.

The accusations against Mr. Khalil were not initially clear. On Sunday evening, the Department of Homeland Security said in a statement that he had been arrested in connection with activities he led that were “aligned to Hamas, a designated terrorist organization.” The statement was reposted by the secretary of state, Marco Rubio.

Karoline Leavitt, the White House press secretary, said at a press briefing on Tuesday that Mr. Rubio was relying on the Immigration and Nationality Act, which gave him broad authority to revoke a green card or a visa from anyone “adversarial to the foreign policy and national security interests” of the United States.

“Mahmoud Khalil was an individual who was given the privilege of coming to this country to study at one of our nation’s finest universities and colleges,” Ms. Leavitt said. “And he took advantage of that opportunity, of that privilege by siding with terrorists.”

She claimed that, at the protests Mr. Khalil had led at Columbia “pro-Hamas propaganda fliers” stamped with the organization’s logo were distributed. She declined to share the fliers with reporters, saying that doing so would corrupt the dignity of the White House briefing room.

It was not clear whether Ms. Leavitt was accusing Mr. Khalil personally of distributing the fliers, and she did not respond to an email requesting clarification.

Mr. Khalil was one of the student leaders of the demonstrations at Columbia, which set off fierce conflict. On one side were critics of Israel’s deadly war in Gaza, where tens of thousands have been killed, and on the other those who argued that the protests were antisemitic, threatening the safety of Jews on campus.

According to a declaration filed in federal court by one of Mr. Khalil’s lawyers, Amy Greer, Mr. Khalil on Friday alerted the Columbia administration about threats against him by online critics calling for his deportation. The following evening, he called Ms. Greer and told her he was surrounded by agents from the Department of Homeland Security.

Ms. Greer said that the agents told her they had a warrant to revoke a student visa. When she informed them that Mr. Khalil did not have a visa, given that he was a permanent resident, he said that the department had revoked the green card.

Ms. Greer filed the petition questioning Mr. Khalil’s detention early Sunday morning. By Sunday afternoon, she was informed that he was being transferred to Louisiana, known for what Elora Mukherjee, the director of the Immigrants’ Rights Clinic at Columbia Law School, characterized as “atrocious detention conditions.”

Ms. Leavitt in her press briefing echoed a warning from President Trump this week, saying that Mr. Khalil was only the first to be targeted. She said that Columbia had the names of others who had “engaged in pro-Hamas activity” and that the school was “refusing to help” the Homeland Security Department identify them.

Mr. Trump, she said, “is not going to tolerate that and we expect all America’s colleges and universities to comply with this administration’s policy.”