Susan Crawford, who is charged with deciding whether to bring Guantanamo detainees to trial, told The Washington Post that US interrogators had tortured Saudi terror suspect Mohammed Al Qahtani.
"We tortured Qahtani," she said, thus becoming the first senior Bush administration official to publicly state that a detainee was tortured.
"His treatment met the legal definition of torture. And that's why I did not refer the case" for prosecution said Crawford, who is the convening authority of military commissions, a system established by the administration of President George W. Bush to try unlawful enemy combatants.
Crawford said US military interrogators repeatedly subjected Qahtani, 30, to sustained isolation, sleep deprivation and prolonged exposure to cold, leaving him in a "life-threatening condition."
"The techniques they used were all authorised, but the manner in which they applied them was overly aggressive and too persistent," she said.
Qahtani, alleged to be the 20th hijacker in the September 11 attacks, was denied entry to the United States one month before the attacks but was captured in Afghanistan and flown to Guantanamo in January 2002.
"There is credible evidence the FBI has had that Qahtani was calling (lead 9/11 hijacker) Mohammed Atta when he arrived in Miami," security analyst Sarah Mendelson told AFP, adding that he could still be brought to trial under such evidence.
"I think it is important to understand that evidence gathered completely separately from harsh interrogation, torture, is the base for bringing a trial against Qahtani," added Mendelson, who directs the human rights and national security project at the Center for Strategic and International Studies.
Qahtani was interrogated over 50 days from November 2002 to January 2003, although he was held in isolation until April 2003, according to the Post.
A Pentagon spokesman said the interrogation techniques used on Qahtani were authorised by former defense secretary Donald Rumsfeld and subsequent reviews found them to be lawful.
"However, the department did adopt a new and more restrictive policy, as well as improved oversight procedures for interrogations and detention operations," said Bryan Whitman.
"While some of the aggressive questioning techniques used on Qahtani were permissible at the time, they are no longer allowed in accordance with the updated army field manual."
Meanwhile, White House spokeswoman Dana Perino reiterated the Bush administration's position that "it has never been the policy of this president or this administration to torture."
The timing of the comments by Crawford, just days before president-elect Barack Obama will be sworn in on January 20, also raised some questions. Obama has vowed to close the controversial detention facility.
"Is she making an argument now because she's worried about a future prosecution of US officials? The timing of the article is hot. The timing of the admission is hot," Mendelson said.
Crawford, a retired judge who previously served as Pentagon inspector general, dismissed war crimes charges against Qahtani in May 2008.
She said she was unaware of whether the other five alleged 9/11 co-conspirators detained at Guantanamo were tortured. "I assume torture," she acknowledged.
Outgoing Vice President Dick Cheney has acknowledged that alleged 9/11 mastermind Khalid Sheikh Mohammed and two other Guantanamo detainees were subjected to waterboarding, or simulated drowning. But Cheney said he did not believe the interrogation techniques amounted to torture.
Despite Crawford having allowed capital murder charges to go forward against the five detainees, the torture allegations cast doubt over whether the United States will ever prosecute the alleged plotters.
Of the 250 inmates still held at the US naval base at Guantanamo Bay, Cuba, only about 20 have been charged, including the five men accused of helping organise the 9/11 attacks.