The US military says it has identified five incidents in which the Koran was mishandled by American personnel at the Guantanamo Bay prison camp.
Alleged abuse of the Koran sparked protests in Muslim countries
But the jail commander said no credible evidence had been found that the book had been flushed down a toilet.
The denial follows similar allegations against US guards in a 2002 document made public on Wednesday, in which an FBI agent quoted an inmate.
Newsweek also reported the toilet claim, but later retracted it.
The Newsweek report sparked protests across the Muslim world. In Afghanistan riots resulted in the deaths of at least 15 people.
The magazine withdrew its story after saying it could no longer corroborate the report.
The White House rounded on the magazine, saying its report had done "lasting damage" to the US image in the Muslim world.
Deliberate and accidental
The Guantanamo Bay prison commander, Brigadier General Jay Hood, said he had found that the Koran had been mishandled on five occasions since late 2001.
Three of the cases appeared to involve deliberate mishandling, while the other two incidents were apparently accidental, he said.
Four cases involved guards and one an interrogator.
Brig Gen Hood said those involved had not violated the rules in place at the time.
The inmate who made the original allegation about the Koran being flushed down the toilet had retracted it, he said.
A Pentagon spokesman characterised the incidents as mainly inadvertent handling of the Muslim holy book.
More than 500 people are being held at Guantanamo Bay, the US naval base on Cuba, suspected of links to the al-Qaeda network.
Some have been detained for more than three years, but have not been charged.