"He was often hooded and had difficulty breathing," Ali Khan said in the statement. "They also beat him repeatedly, slapping him in the face, and deprived him of sleep."
Khan staged hunger strikes and twice attempted suicide — once cutting through an artery.
Under the plea agreement, Khan has forfeited his right to sue the government over his treatment.
"He was tortured," Dixon said. He said he could not provide details of Khan's allegations, which have been classified — but said the government should.
"That is something that the United States has to address," he said. "The United States has to accept responsibility for what happened to him, just the way that he accepted responsibility for his own actions."
Khan appeared fit and relaxed during his arraignment last week. Dressed in a suit and shorn of the thick beard with which he had been photographed, he was polite and respectful in his responses to Pohl.
He is scheduled to return before the tribunal in four years. Under the agreement, If he has given prosecutors his "full and truthful cooperation," he may be sentenced to no more than 15 more years.
Khan still could be detained as an enemy combatant after his sentence is complete, but would be allowed to petition for his release. Khan told the military judge he understood the terms.
"This agreement does not guarantee that I will be able to get free, even after I do my time," he said. "I'm taking a leap of faith here, sir. That's all I can do."
Dixon said Khan is "materially different" from the other high-value targets at Guantanamo Bay.
"He pleaded guilty to very serious offenses, but he wishes that he had never had any involvement with al-Qaida," Dixon said. "He has made a decision to cooperate with the United States government and to testify, if asked, against al-Qaida — at great risk to himself and his family."
Dixon described the plea "as a reflection of the genuineness of his remorse and his desire to see some measure of redemption."
"It is his hope that by pleading guilty, he will be released some day and he'll be able to see his father again, and see his daughter for the first time."
The Associated Press contributed to this report.
Majid Shoukat Khan
Born Feb. 28, 1980, in Pakistan
Married to Rabia Yaqoob, one child
Arrives with his family in Catonsville in 1996
Graduates from Owings Mills High School in 1999
Works as database administrator for Electronic Data Systems in Tysons Corner, Va.
Watches smoke rise over Pentagon on Sept. 11, 2001
Travels to Pakistan in 2002, gains introduction with Khalid Sheikh Mohammad
Delivers al-Qaida money to finance 2003 bombing of J.W. Marriott hotel in Jakarta
Captured by Pakistani security forces in March 2003, held in secret CIA prison
Transferred to Guantanamo Bay in 2006
Tells military panel in 2007 he has been tortured
Pleads guilty to murder, espionage and conspiracy Feb. 29, 2012; agrees to testify against other terror suspects in exchange for 19-year sentence.