Moheb Ullah Borekzai made the comments Thursday in an interview with The Associated Press, three days after he was freed from the prison camp in Cuba and flown home to Afghanistan.
There have been repeated accusations of Quran abuse at Guantanamo, including an allegation last month by a Russian Muslim cleric formerly held at the prison that guards regularly put the holy book in a toilet, although he said he never witnessed that himself.
Borekzai said that during his three years at Guantanamo he never saw or heard claims from other prisoners of guards abusing the Quran by placing it in toilets. But he said he had seen guards throw the Quran two or three times.
"We would always put the holy Quran in a high place, for example, in a drawer or on a shelf," he said, speaking in a guesthouse in the Afghan capital, Kabul. "They (the guards) would just throw it on the ground or on the bed. ... I, myself, have seen them throwing the Quran."
Such mistreatment of the Quran made the made the prisoners "very angry," he said, adding that late last year guards "changed their procedures."
"The Americans made a promise that U.S. soldiers have no right to touch the Quran ... They announced (it) on loudspeakers," Borekzai said. "There has been no abuse of the Quran since last year."
During Muslim prayer times, guards are now silent and are "not even talking to each other," Borekzai said.
A spokesman at U.S. Southern Command in Miami, which oversees the prison, did not immediately respond to e-mailed questions about Borekzai's comments. In the past, the military has insisted that guards are instructed not to touch the Quran.