The newly released document, dated 1 August 2002, contained a summary of statements made days earlier by a detainee, whose name was redacted, in two interviews with an FBI special agent, whose name also was withheld, at the Guantanamo prison for foreign terrorism suspects.
"Personally, he has nothing against the United States. The guards in the detention facility do not treat him well. Their behavior is bad. About five months ago, the guards beat the detainees. They flushed a Quran in the toilet," the FBI agent wrote.
The document that was written in 2002 and made public on Wednesday was rejected by the Pentagon, which described the allegation as not credible.
"It's not credible," chief Pentagon spokesman Lawrence Di Rita said of the allegation regarding a Quran in a toilet.
Di Rita said that the US military questioned the detainee on 14 May and that the man was "very cooperative and answered the questions but did not corroborate the allegation recorded on Aug. 1, 2002".
Di Rita said he did not know whether the man actually recanted the allegation.
The declassified document's release came the week after the Bush administration denounced as wrong a 9 May Newsweek article that stated US interrogators at Guantanamo had flushed a Quran down a toilet to try to make detainees talk.
The magazine retracted the article, which had triggered protests in Afghanistan in which 16 people died.