The US commander at Guantanamo, Brigadier-General Jay Hood, refused to specify the nature of the mishandling of the Koran, but did say it was not flushed down a toilet at any stage.
He said investigators did not directly ask a detainee about an allegation reportedly made in an August 2002 document that guards flushed a Koran in the toilet.
But he told a Pentagon briefing: “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 Koran down a toilet.”
Brig. Hood said two US Guantanamo staffers have been disciplined, with one transferred to other duties.
He opened the inquiry following deadly riots in Afghanistan earlier this month, triggered by a Newsweek article claiming investigators interrogating Muslim detainees at Guantanamo had flushed a Koran down a toilet.
Newsweek later retracted the story after its main source backed away from the allegations.
Initial findings from the military inquiry, which began 12 days ago, detailed 13 allegations of Koran mishandling, with five confirmed cases of “what could be broadly defined as mishandling of a Koran”.
Four US guards and one interrogator were involved in the cases, three of which appeared to be deliberate mishandling and two accidental, Mr Hood said.
Four of the five cases occurred before written guidelines on how to handle the Koran at Guantanamo were issued in January 2003.
An FBI report in 2002 said: “The guards in the detention facility do not treat him well. Their behaviour is bad. About five months ago, the guards beat the detainees. They flushed a Koran in the toilet.”
Mr Hood said he became aware of the report within 48 hours of opening his investigations.
Investigators reviewed interrogations logs and other documents to find out what happened.
In six of the 13 incidents, a guard “either accidentally touched a Koran, touched it within the scope of his duties, or did not accidentally touch the Koran at all,” he said.
“We considered each of these incidents resolved.”
No details were given on the specific instances of mishandling, saying the investigation is still underway.
More than 500 people are being held at a US military base at Guantanamo Bay, Cuba, suspected of links to the al-Qaeda terrorism network.