US District Judge Joyce Hens Green on Thursday also agreed that Washington can appeal another ruling that military tribunals to review detainee cases were constitutionally flawed.
Green additionally put on hold her ruling so it would not take effect immediately while the administration appealed to the US Court of Appeals.
In a sharp rebuke for the administration, Green had ruled on Monday that the prisoners at the US military base at Guantanamo Bay in Cuba have the constitutional right not to be deprived of liberty without due process of law.
She ruled that the special military tribunals to determine the status of each Guantanamo detainee as an "enemy combatant" failed to satisfy constitutional requirements.
Green ruled the procedures failed to give the detainees access to material evidence and failed to let lawyers help them when the government refused to disclose classified information.
The ruling stemmed from the 7 July 2004 order by Deputy Defence Secretary Paul Wolfowitz which created the Combatant Status Review Tribunal to determine whether each Guantanamo detainee had been correctly found to be an "enemy combatant".
Meanwhile, the US Navy has ruled that three more Guantanamo prisoners had been wrongly classified as enemy combatants, using the tribunal process that Judge Green found constitutionally flawed.
It brought to six the number of detainees found not to be enemy combatants since the US began sending terrorism suspects to Guantanamo Bay three years ago.
Pentagon spokesman Lieutenant-Commander Daryl Borgquist would not identify the three or their nationalities but said the State Department would arrange for them to go home.
So far the tribunals have ruled that 387 other Guantanamo prisoners were correctly classified as enemy combatants.