A military judge at the U.S. naval base in Guantanamo Bay on Thursday rejected a White House request to suspend a hearing for a USS Cole bombing suspect, creating an unexpected challenge for the Obama administration as it reviews the U.S. war-crimes trials process.

The judge, army Col. James Pohl, said his decision was difficult but necessary to protect "the public interest in a speedy trial."

The ruling came in the case against Abd al-Rahim al-Nashiri, the alleged mastermind of the 2000 navy destroyer bombing that killed 17 U.S. sailors in Yemen.

It seemed to take the Pentagon completely by surprise.

"The Department of Defence is currently reviewing Judge Pohl's ruling," said navy Cmdr. Jeffrey Gordon, a Pentagon spokesman. "We will be in compliance with the president's orders regarding Guantanamo."

U.S. President Barack Obama has ordered the closure of the detention centre in Cuba within a year.

The administration asked last week for a 120-day suspension in proceedings against some 20 detainees, including Canadian Omar Khadr, as it considers whether to continue trying terrorism suspects in the military commissions, revamp them or try suspects in other courts.

"On its face, the request to delay the arraignment is not reasonable," Pohl wrote in his ruling.

Navy Lt.-Cmdr. Stephen Reyes, the Pentagon-appointed lawyer for Abd al-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. "I have no idea what they're going to do."

Pohl is the chief judge at the tribunals. At least two other judges have already granted the continuance sought by the president, and the defence and prosecution agreed they should be suspended.