The treatment of inmates at the prison has outraged human rights groups
A military judge at the Guanatanamo Bay detention facility has rejected a request by US President Barack Obama to suspend the trial of a detainee.
Correspondents say this could be a setback to Mr Obama's plans to close the facility.
Abd al-Rahim al-Nashiri, a Saudi citizen, is accused of planning the USS Cole attack of October 2000.
The White House said it was consulting the Pentagon and justice department about its possible options.
Judge James Pohl said the request to halt the trial to allow a review by the new administration was "unpersuasive".
The trial of Mr Nashiri will go ahead, he ruled
Abd al-Rahim al-Nashiri has said he was tortured into confessing
In one of its first actions, the Obama administration instructed prosecutors to ask for the trials of 21 detainees who had been charged to be delayed by 120 days.
In some cases, the request was quickly granted.
The attack on the USS Cole while it was moored off Yemen left 17 US service personnel dead and 50 injured.
Mr Nashiri was arrested in the United Arab Emirates in 2002 and eventually transferred to Guantanamo.
He allegedly conspired to help two Islamic militants who steered an explosives-laden barge alongside the ship.
The new administration will now have to decide how to proceed, correspondents say.
Mr Obama ordered the review of military trials for terrorism suspects last week. He also ordered the closure, within one year, of the Guantanamo detention centre.
He said the US would continue to fight terrorism but would maintain its "values and ideals" as well.
Some 250 inmates accused of having links to terrorism remain in the facility.
The legal process for these prisoners has been widely criticised because the US military acts as jailer, judge and jury.
A judge has already suspended for 120 days the trial of five men accused over the 9/11 attacks.
These include alleged mastermind Khalid Sheikh Mohammed, who opposed the suspension, saying he wanted to confess to his role in the attacks.
"I believe that all the other trials were stayed, which I think continues to give us what we need to evaluate who is at Gitmo [Guantanamo] and make the decisions commensurate with the executive order that the president signed," White House spokesman Robert Gibbs said after Thursday's ruling.