NEW YORK — NEW YORK — The Trump administration said Friday it does not plan to free recent Columbia University graduate and Palestinian activist Mahmoud Khalil from a Louisiana detention center, despite missing a morning deadline to challenge his release in federal court.

New Jersey Federal Judge Michael Farbiarz on Wednesday granted Khalil’s request to stop the government from detaining and deporting him — for now — based on Secretary of State Marco Rubio’s determination that his pro-Palestinian advocacy compromises a “compelling” U.S. foreign policy interest, meaning U.S. support for Israel.

The judge said the order wouldn’t go into effect until Friday at 9:30 a.m., giving the government time to file a notice of appeal challenging his finding.

“The deadline has come and gone and Mahmoud Khalil must be released immediately,” Khalil’s lawyers said in a statement to the Daily News earlier Friday. “Anything further is an attempt to prolong his unconstitutional, arbitrary, and cruel detention.”

In response to Khalil’s legal team’s Friday morning filings, the federal government said they haven’t sought to stay the ruling because they don’t interpret the judge’s Wednesday order as requiring immigration authorities to release Khalil.

“The Court did not order Respondents to release Petitioner Mahmoud Khalil,” the government lawyers wrote in court documents. “The Court instead enjoined Respondents from detaining Khalil ‘based on the Secretary of State’s determination.’ That injunction does not interfere with Respondents’ authority to detain Khalil on other grounds.”

The government is now detaining Khalil on allegations that when he applied for lawful permanent residency in 2024, he didn’t disclose membership in UNRWA, that he’d worked for the British Embassy in Beirut, or that he was a member of Columbia University Apartheid Divest. His lawyers have called the allegations baseless.

Spokespeople for the Department of Homeland Security and the Justice Department did not immediately respond to requests seeking comment.

In a statement Wednesday, DHS Assistant Secretary Tricia McLaughlin had indicated the government would challenge Farbiarz’s order, saying it “delays justice and seeks to undermine [Trump’s] constitutionally vested powers.” McLaughlin said a green card was a privilege that should be revoked for people who support terrorist activity, an allegation the Trump admin has levied against Khalil without backing up.

The 30-year-old grad student, a legal permanent resident, has been detained in Jena, Louisiana, since March 9, a day after agents from DHS took him into custody at his Columbia-owned apartment.

In the weeks that followed, the government cited an obscure provision in a 1952 immigration law finding the office of the secretary of state can order someone deported if their beliefs could unfavorably impact U.S. foreign relations, namely, the government’s policy of combating antisemitism. Khalil, a Palestinian who grew up in a Syrian refugee camp, rejects that his advocacy for civilians in war-torn Gaza and the West Bank is based on bigotry.

His lawyers have pointed to public comments he made well before his arrest condemning antisemitism.

Farbiarz’s Wednesday opinion and order found his detention jeopardized his reputation and right to free speech.

“[The] Court finds as a matter of fact that [Khalil’s] career and reputation are being damaged and his speech is being chilled,” Farbiarz wrote Wednesday, “and this adds up to irreparable harm.”

The government has also cited another basis for Khalil’s deportation in alleging that he failed to fill out forms when he applied for residency accurately. But the federal judge so far has been suspicious of that reasoning for Khalil’s detention.

Farbiarz noted Wednesday that the government “virtually never [detains]” people on such allegations and that Khalil’s ongoing detention was, by all accounts, driven by Rubio’s unconstitutional policy.

In response, the federal government on Friday argued that while the court found it was unlikely that Khalil would be detained on another basis, the federal judge did not explicitly say it would be unlawful to do so. They concluded that Khalil is now being held on the secondary charge.

The government lawyers also asked the court that if it isn’t convinced by their argument to stay any order to release Khalil pending appeal or set a date for the order to go into effect a week later.

Khalil, whose U.S. citizen wife accepted his diploma from Columbia on his behalf last month, is fighting his detention and deportation in a habeas corpus case filed in New Jersey, where he was swiftly transferred after being taken into custody.

He played a prominent role in campus protests against Israeli military activity in Gaza and the West Bank and Columbia’s financial ties to Israel, acting as a mediator between students and the school administration.

Separately, he’s faced immigration proceedings in Louisiana, where Judge Jamee Comans has sided with the government in ordering him deported. Before a hearing in that matter last month, where Khalil and other witnesses sought to convince Comans that his deportation could result in his death, he met his 1-month-old son, Deen, for the first time, who was born weeks after he was detained.

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