The investigation also found 15 incidents in which detainees mishandled or inappropriately treated the Quran, including one case of a detainee ripping pages from his holy book, Brig. Gen. Jay W. Hood, the Guantanamo Bay prison commander who led the investigation, told reporters Thursday.
Meanwhile, Muslims from Dhaka to Jakarta rallied Friday to protest the alleged desecration of Islam's holy book by burning U.S. flags and throwing tomatoes at a likeness of President Bush.
More than 15,000 people took to the streets of Pakistan's largest cities. Thousands more rallied in Bangladesh, Malaysia, Indonesia and Kashmir, where police fired teargas and used batons to disperse a crowd of several hundred.
Hood emphasized that his probe is not yet complete. It was launched about two weeks ago in response to a Newsweek magazine story that said U.S. officials had confirmed a Quran was flushed in a toilet. The story stirred worldwide controversy and the Bush administration blamed it for deadly demonstrations in Afghanistan.
Newsweek later retracted its report.
Hood, who has commanded the U.S. naval prison compound in Cuba since March 2004, told a Pentagon news conference that 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 May 14, 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 had heard fellow inmates talk of being beaten or otherwise mistreated.
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 an Aug. 1, 2002, FBI summary of an FBI agent's July 22, 2002, interrogation of the prisoner. A partly redacted version of the summary was made public this week.
"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.
Other prisoners who were returned to their home countries after serving time at Guantanamo Bay as terror suspects have alleged Quran desecration by U.S. guards, and some have said a Quran was placed in 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.
Lawrence Di Rita, spokesman for Defense Secretary Donald H. Rumsfeld, said at the news conference with Hood that at this point it should be clear that any mishandling of the Quran was largely inadvertent.
"I think it's safe to say that the policies and procedures down there are extraordinarily careful, and they're — as I said — policies that we've released, and people can judge for themselves. But I think people will see that the atmosphere down there is one of great respect for the practice of faith by detainees," he said.
Michael O'Hanlon, a senior fellow in foreign policy studies at the Brookings Institution, said on CBS News' The Early Show that the revelations are serious and he compared it to rubbing salt in a wound in the Muslim world.
"But I don't think these particular allegations are of particular concern as opposed to the Guantanamo Bay and Abu Ghraib issues," O'Hanlon told Early Show co-anchor Hannah Storm. "But it appears here some American military officers may have touched the Quran when they are not supposed to because non-believers are not supposed to touch the Quran. Early on there were not clear procedures."
The protest in Islamabad, Pakistan's capital, began in a tense atmosphere just hours after aat an annual celebration.
"It's time for Muslims to unite," Qazi Hussain Ahmed, head of a religious alliance that organized many of the rallies, told a crowd of more than 5,000. "We have been given a challenge."
He said more rallies were planned Friday in London, Washington D.C., New York, Chicago, Iraq, Palestine and Syria.
In the southwestern city of Quetta, 5,000 demonstrators chanted slogans against the United States and Britain. Another 5,000 gathered in the southern city of Karachi, demanding the expulsion of the U.S. ambassador.
Several hundred Muslims rallied in Malaysia, waving placards reading "Long Live Islam" and burning U.S. and Israeli national flags outside the U.S. Embassy. A smaller rally was held in Srinagar, the Indian-held capital of Kashmir.
In Indonesia, the world's most populous Muslim country, a small crowd of protesters in the capital of Jakarta tossed tomatoes at a portrait of Bush.
"No one has the right to debase our holy book. We are prepared to die to protect the honor of our religion," Fazlul Huq Amini, a lawmaker from Islamic Oikya Jote, told a crowd of several thousand at a rally in Dhaka, Bangladesh.
No violence was reported at any of the protests, which were organized before the officials' comments in Washington D.C. on Thursday.