An inmate at the Guantanamo Bay prison camp accused US guards of flushing a Koran down the toilet in 2002, newly declassified FBI documents reveal.
More than 500 detainees are held at Guantanamo
The disclosure follows a row over a similar claim made in Newsweek, which the magazine was forced to retract.
The Newsweek report sparked protests across the Muslim world, and riots in Afghanistan that killed 15 people.
The Pentagon said last week it had seen "no credible and specific allegations" about putting a Koran in a toilet.
Newsweek last week apologised for, and then retracted its report, after saying it could no longer corroborate the story.
The White House rounded on the magazine, saying its report had done "lasting damage" to the US image in the Muslim world.
But the FBI documents made public on Wednesday, after a request from the human rights group American Civil Liberties Union (ACLU), show that such allegations had been made at Guantanamo Bay.
After interviewing a detainee, an unnamed FBI agent wrote on 1 August 2002: "Personally, he has nothing against the United States. 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.
"The guards dance around when the detainees are trying to pray. The guards still do these things."
The ACLU said the documents showed the Pentagon was aware of such allegations being made at Guantanamo Bay long ago, but had repeatedly turned a blind eye to "mounting evidence of widespread abuse".
The Pentagon did not immediately comment on the documents, but officials have said recently that various claims made by former detainees have been proved false.
Protests against alleged US abuse of the Koran continue
Officials say they have begun comparing detainee complaints to see if any are corroborated.
ACLU lawyer Jameel Jaffer said: "Unfortunately, one thing we've learned over the last couple of years is that detainee statements about their treatment at Guantanamo and other detention centres sometimes have turned out to be more credible than US government statements."
Other FBI documents released on Wednesday detailed further accusations, including one by a detainee who said a female interrogator wiped his face with her menstrual blood.
Meanwhile Amnesty International urged the US to shut Guantanamo Bay, calling it "the gulag of our time".
In a report the group said the US had undermined human rights across the world, by trying to "redefine and sanitise torture".
The White House dismissed the report as "ridiculous and unsupported".
Spokesman Scott McClellan said allegations of mistreatment were being investigated.
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.