By Andy Rose, Dalia Faheid, CNN

(CNN) — Mahmoud Khalil’s hopes of being freed on bond as he continues fighting the Trump administration’s efforts to deport him were dashed Friday, despite a judge saying the government could no longer hold Khalil on the premise that his presence in the country is against the national interest.

Judge Michael Farbiarz said the determination by Secretary of State Marco Rubio that the Palestinian activist and Columbia University graduate student’s presence in the country had “potentially serious adverse foreign policy consequences for the United States” was likely unconstitutional.

But attorneys for the Department of Justice said the judge’s decision did not prevent them from continuing to hold Khalil on a second claim – that he failed to give required information in his application to become a legal permanent resident of the US, in their response letter to the judge on Friday.

Farbiarz did not specifically strike down that charge as a reason for detaining Khalil – a distinction the Trump administration is seizing on – and on Friday the judge ruled that the administration’s interpretation of his order is correct.

Farbiarz denied Khalil’s request for relief on Friday afternoon, saying his legal team “did not put forward factual evidence as to why it might be unlawful to detain him on the second charge.”

Khalil, who played a central role in negotiations on behalf of pro-Palestinian student protesters last year, has not been charged with a crime.

The lawful permanent resident – who is also married to a US citizen – now remains at the Louisiana ICE detention center, where he has been held for more than three months after he was arrested outside his apartment on Columbia University’s campus in March. He has missed out on several milestones due to his detainment: notably the birth of his first child in April and his Columbia graduation.

After the judge’s Friday ruling, one of Khalil’s attorneys, Amy Greer, said the administration is “now using cruel, transparent delay tactics to keep him away from his wife and newborn son ahead of their first Father’s Day as a family.”

“Instead of celebrating together, he is languishing in ICE detention as punishment for his advocacy on behalf of his fellow Palestinians. It is unjust, it is shocking, and it is disgraceful,” Greer said in a statement.

Khalil was among the first arrestees in the Trump administration’s immigration crackdown targeting student activism. In the nearly 100 days since his arrest, at least three other international college students have been released from detention after weeks of legal action by their attorneys. Khalil’s case, in contrast, has dragged on for months in a federal district court in New Jersey and an administrative immigration court in Louisiana.

The administration had been given until 9:30 a.m. Friday to file an appeal, or else the preliminary injunction would go into effect. No appeal was filed Friday, and Khalil’s attorneys demanded his release.

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

The Syrian-born Palestinian refugee is one of several foreign nationals the Trump administration has accused of posing a national security threat due to alleged ties to terrorist organizations – a claim his attorneys have repeatedly disputed.

His detention has sparked protests across the country from supporters who believe his detention is a flagrant violation of core American values, including the protection of free speech.

The administration has relied on an obscure section of US law to argue that Khalil should be deported because his presence in the United States threatens the administration’s foreign policy goal of combatting antisemitism.

His lawyers, meanwhile, challenged the legality of Khalil’s detention and contend he was targeted for his pro-Palestinian views in violation of his constitutional rights. They argue the government’s evidence is insufficient and based solely on a letter from Secretary of State Marco Rubio that does not allege criminal activity.

This is a developing story and will be updated.

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CNN’s Gloria Pazmino contributed to this report.