The White House said on Thursday it was looking at its options following the judge's ruling.
"We are consulting with the Pentagon and the department of justice to explore our options in that case," Robert Gibbs, a White House spokesman, said.
At least two other judges have already granted the delay sought by the president, with the defence and prosecution agreeing in both cases that they should be suspended.
|Seventeen US sailors were killed in
the attack on the USS Cole [GALLO/GETTY]
Navy Lieutenant Commander Stephen Reyes, the Pentagon-appointed lawyer for Abdal-Rahim al-Nashiri, said the decision gives the Obama administration few options.
"The next step, if the government wants to halt the proceedings, is to withdraw the charges," Reyes said.
"Now it's in the government's hands," he said.
Obama has ordered the detention centre in Cuba to be closed within a year.
Al-Nashiri is charged with conspiring with al-Qaeda to send an explosives-laden boat into the side of the USS Cole in the Yemeni port of Aden in 2000.
The attack killed 17 US sailors and al-Nashiri could face the death penalty if convicted.