Mohammad al-Qahtani was a suspect in the first capital case at Guantanamo
US agents at Guantanamo Bay tortured a Saudi man suspected of involvement in the 11 September attacks, the official overseeing trials at the camp has said.
Susan Crawford told the Washington Post newspaper that Mohammad al-Qahtani had been left in a "life-threatening condition" after being interrogated.
The Pentagon said their methods were legal in 2002, when the interviews took place - though some were now banned.
Mr Qahtani remains at Guantanamo, but all charges against him were dropped.
He had been facing trial on counts of conspiracy, terrorism, and murder in violation of the laws of war.
Although officials gave no reason for halting the prosecution in May 2008, Ms Crawford said in her interview that the decision had been taken because of the methods used by US agents.
She said Mr Qahtani had been subjected to sustained periods of cold, isolation and sleep deprivation.
"His treatment met the legal definition of torture. And that's why I did not refer the case," she said.
Ms Crawford, who was appointed convening authority for military commissions in February 2007, said Mr Qahtani had been interrogated for 18 to 20 hours a day almost continuously for eight weeks.
"The techniques they used were all authorised, but the manner in which they applied them was overly aggressive and too persistent," she said.
In a statement, the Pentagon said it had carried out more than a dozen reviews of its operations - including the detention of Mr Qahtani.
"They concluded the interrogation methods used at [Guantanamo], including the special techniques used on Qahtani in 2002, were lawful," the statement said.
"However, subsequent to those reviews, the Department adopted new and more restrictive policies.
"Some of the aggressive questioning techniques used on Qahtani, although permissible at the time, are no longer allowed in the updated army field manual."
In her newspaper interview, Ms Crawford said she was shocked, upset and embarrassed by the treatment of the detainee.
She said: "If we tolerate this and allow it, then how can we object when our servicemen and women, or others in foreign service, are captured and subjected to the same techniques?
"How can we complain? Where is our moral authority to complain? Well, we may have lost it."
According to a report by Amnesty International, Mr Qahtani was at various times forced to wear women's clothes and was tied by a lead and forced to perform animal tricks.
And the document, published last May, also contained allegations that dogs had been used on two occasions to "terrorise" the detainee.
Mr Qahtani has been in detention at Guantanamo since 2002, after being picked up in Afghanistan.
The US authorities had accused him of intending to take part in the 11 September attacks, and he was labelled the "20th hijacker".
He had tried to travel to the US in August 2001, but had been refused entry.
Despite her decision to drop the prosecution, Ms Crawford said Mr Qahtani remained a "very dangerous man".
"There's no doubt in my mind he would have been on one of those planes had he gained access to the country in August 2001," she said.
Earlier this week, advisers to president-elect Barack Obama confirmed he would issue an order for the closure of Guantanamo Bay within days of taking office.
But no decision has yet been announced on the future of Mr Qahtani and other inmates who are deemed too dangerous to release, but may be impossible to prosecute.