In other confirmed incidents, prison guards threw water balloons into a cell block to cause an unspecified number of Qurans to get wet; a guard's urine splashed on a detainee and his Quran; an interrogator stepped on a Quran during an interrogation; and a two-word obscenity was written in English on the inside cover of a Quran.
The findings are among results of an investigation last month by Brigadier-General Jay Hood, commander of the detention centre in southeastern Cuba, that was triggered by a Newsweek magazine report - later retracted - that a US soldier had flushed a Guantanamo Bay detainee's Quran down a toilet.
The story stirred worldwide controversy, and the Bush administration blamed it for demonstrations in Afghanistan that killed at least 16 people.
Last week, Hood disclosed he had confirmed five cases of mishandling of the Quran, but he refused to provide details.
In the incident involving urine, which took place in March, Southern Command said a guard left his post and urinated near an air vent and "the wind blew his urine through the vent" and into a cell block.
Guantanamo prisoners said the
desecrations began in 2002
It said a detainee told guards the urine "splashed on him and his Quran". The statement said the detainee was given a new prison uniform and Quran, and that the guard was reprimanded and given duty in which he had no contact with prisoners.
Southern Command said a civilian contractor interrogator, who was later fired, apologised in July 2003 to a detainee for stepping on his Quran.
In August 2003, prisoners' Qurans became wet when night-shift guards threw water balloons in a cell block, the statement said. In February 2002, guards kicked a prisoner's Quran, it added.
In the fifth confirmed incident of mishandling a Quran, Southern Command said a prisoner in August 2003 complained that a two-word obscenity had been written in English in his Quran.
Southern Command said it was possible a guard had written the words, but equally possible the prisoner himself had done, but they did not offer any explanation of his possible motive.
Allegations of Quran desecration at Guantanamo Bay have stirred anti-American passions in many Muslim nations.
Pentagon officials have insisted the problems were relatively minor, and US commanders have gone to great lengths to enable detainees to practice their religion in captivity.
Iraqis walk on US and Israeli
flags in protest
Hood said last week he found no credible evidence a Quran was ever flushed down a toilet. He said a prisoner who was reported to have complained to an FBI agent in 2002 that a military guard threw a Quran in the toilet has since told Hood's investigators that he never witnessed any form of Quran desecration.
The unidentified prisoner, re-interviewed at Guantanamo on 14 May, said he had heard talk of guards mishandling religious articles but did not witness any such acts, Hood said.
The prisoner also stated that he personally had not been mistreated but that he heard fellow inmates talk of being beaten or otherwise mistreated.
The Pentagon says there is no
evidence of flushing of the Quran
The general said he could not speculate on why the prisoner did not repeat his earlier statement about a guard flushing a Quran in a toilet. The statement was contained in a 1 August 2002 FBI summary of an FBI agent's 22 July interrogation of the prisoner. A revised version of the summary was made public this week.
The prisoner did not specifically recant his earlier allegation, since Hood said the prisoner was not asked in the 14 May interview whether he had made the specific statement in 2002 as reported by the FBI. Instead he was asked more broadly whether he had seen the Quran "defiled, desecrated or mishandled".
"He allowed as how he hadn't, but he heard that guards at some other point in time had done this," Hood said, adding that this allegation from the 2002 FBI report was the only one Hood found that involved a toilet.
"I'd like you to know that we have found no credible evidence that a member of the Joint Task Force at Guantanamo Bay ever flushed a Quran down a toilet," Hood said.
"We did identify 13 incidents of alleged mishandling of the Quran by Joint Task Force personnel. Ten of those were by a guard and three by interrogators."
Of the 13 alleged incidents, five were substantiated, he said. Four were by guards and one was by an interrogator. Hood said the five cases "could be broadly defined as mishandling" of the holy book, but he refused to discuss details.
In three of the five cases, the mishandling appears to have been deliberate. In the other two, it apparently was accidental.