updated 1/29/2009 6:46:42 PM ET 2009-01-29T23:46:42

A military judge at Guantanamo 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.

"We just learned of the ruling ... and we are consulting with the Pentagon and the Department of Justice to explore our options in the case," said White Press secretary Robert Gibbs, adding that he doubted the decision would hamper the administration's ability to decide how to move forward from Guantanamo.

The Department of Defense is reviewing Judge Pohl's ruling, said Navy Cmdr. Jeffrey Gordon, a Pentagon spokesman.

Geoff Morrell, another Pentagon spokesman, told reporters that there were "no ifs, ands or buts" about adhering to the president's executive order and that there would "be no proceedings continuing down at Gitmo with military commissions."

"The bottom line is, we all work for the president of the United States in this chain of command, and he has signed an executive order which has made abundantly clear that until these reviews are done all of this is on hiatus," Morrell said.

Delay 'not reasonable'
President Barack Obama has ordered the detention center in Cuba to be closed within a year. The administration asked last week for a 120-day suspension in proceedings against some 20 detainees as it considers whether to continue trying alleged terrorists in the military commissions, revamp them or try suspects in other courts.

Obama signed an executive order directing Defense Secretary Robert Gates to ensure that "all proceedings of such military commissions to which charges have been referred but in which no judgment has been rendered ... are halted."

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

The American Civil Liberties Union urged Gates to put a halt to the proceedings by withdrawing the charges against al-Nashiri.

"Judge Pohl's decision to move forward despite a clear statement from the president also raises questions about Secretary of Defense Gates — is he the 'new Gates' or is he the same old Gates under a new president?" ACLU Executive Director Anthony Romero said. "Secretary Gates has the power to stop the military commissions and ought to follow his new boss' directives."

The Cole's former commanding officer, retired Navy Cmdr. Kirk Lippold, said the case "needs to go forward" at Guantanamo. He said Pohl's ruling validated the war-crimes trials by demonstrating the independence of the military judges.

"The families involved want to see al-Nashiri held accountable for his heinous acts," Lippold said in an interview.

Limited options
Navy Lt. Cmdr. Stephen Reyes, the Pentagon-appointed attorney 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 the U.S. Navy base in Guantanamo Bay, Cuba. At least two other judges have already granted the continuance sought by the president, and the defense and prosecution agreed they should be suspended.

Pohl noted that no substantive legal issues would be litigated at al-Nashiri's arraignment, scheduled for Feb. 9, meaning that "nothing will be mooted or necessary for relitigation" if Obama scraps the tribunals.

Abrupt halt
The war crimes court came to an abrupt halt Jan. 21 after two other military judges granted Obama's request for a suspension. His executive order came the following day in Washington.

Those cases were against a Canadian accused of killing a U.S. soldier in Afghanistan and five men charged in the Sept. 11 attacks.

In all, war crimes charges are pending against 21 men at Guantanamo. Before Obama became president, the U.S. said it planned to try dozens of detainees in a system that was created by George W. Bush and Congress in 2006 and has faced repeated challenges.

Last week, Obama also ordered the CIA to close down secret overseas prisons and the Pentagon to close down the Guantanamo prison within a year. The president also banned the harshest interrogation methods.

Revamping security policy
The CIA has used secret "black site" prisons around the world to question terror suspects, usually plucking them from one country and moving them to another where U.S. agents operated a prison. A senior White House source said the CIA will be allowed to continue these "renditions" but not to countries that torture and not to its own prisons.

"We intend to win this fight," Obama said of the war on terrorism. "We're going to win it on our terms." But he also said he didn't want to have to make a "false choice" between successfully waging war against terrorist organizations and hewing to U.S. human rights ideals in the process.

"This is following through not just on a commitment I made during the campaign but an understanding that dates back to our Founding Fathers, that we are willing to observe core standards of conduct — not just when it's easy but also when it's hard," the president said.

© 2012 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

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