Newark, New Jersey-based US District Judge Michael Farbiarz on Wednesday said the government could not use foreign policy interests to justify Khalil's detention.
On Friday the government said it was also holding Khalil, a legal permanent resident of the United States, on a charge of immigration fraud.
In response, Farbiarz said Khalil's lawyers had not successfully argued why it was unlawful for the government to hold him on the charge, which he has denied.
The ruling marked the latest turn in Khalil's fight to be freed from a Louisiana detention centre after his March arrest for involvement in the pro-Palestinian protest movement, which President Donald Trump has called anti-Semitic.
His detention was condemned by civil rights groups as an attack on protected political speech.
Marc Van Der Hout, a lawyer for Khalil, said the government practically never detained people for immigration fraud and the Syrian-born student was being punished for opposing Israel's US-backed war in Gaza following Hamas' October 2023 attack.
"Detaining someone on a charge like this is highly unusual and frankly outrageous," Van Der Hout said.
"There continues to be no constitutional basis for his detention."
Farbiarz had previously suggested legal residents like Khalil were rarely detained on the basis of immigration fraud.
On Friday, he said Khalil should seek bail from the immigration lawyer in his case.
As lawyers for the Syrian-born activist sought his release, Kilmar Abrego Garcia, another immigrant targeted by the Trump administration, pleaded not guilty to migrant smuggling charges after his wrongful deportation.
Khalil, a graduate student at Columbia's School of International and Public Affairs, was arrested by immigration agents in the lobby of his university residence in Manhattan on March 8.
His US citizen wife, Dr Noor Abdalla, gave birth to the couple's first child while Khalil was detained in April.
