Details of the five confirmed cases of mishandling of the Islamic holy book were released by Brigadier-General Jay Hood, commander of the prison. This contradicted earlier claims by the Pentagon that there were no “credible” allegations of abuse there.

A story last month in Newsweek magazine, later retracted, that a copy of the Koran had been flushed down a lavatory at the facility, led to rioting in Afghanistan that left at least 16 people dead and put America on the defensive.

In the most recent and bizarre of the incidents detailed in the army’s report, a guard splashed a detainee and his Koran with urine in March this year. “The guard had left his observation post and went outside to urinate,” the report found. “He urinated near an air vent and the air blew his urine through the vent into the block.” He was reassigned to other duties.

The report found that an investigator had stood on a Koran while questioning a detainee. He was fired for “a pattern of unacceptable behaviour”. Guards on a night shift threw water balloons, soaking a number of the holy books. In another incident a guard kicked a Koran in a detainee’s cell.

A two-word obscenity was scrawled in a Koran, but it was not clear whether a guard or prisoner wrote it. The report found 19 incidents of abuse of the book by detainees.

Hood said there was a “consistent, documented policy of respectful handling of the Koran” — 1,600 of which had been handed to the predominantly Muslim internees — at the facility.

The release of the report came amid a continuing row over treatment of detainees at Guantanamo Bay following a report by Amnesty International branding it “the gulag of our times”.

President George W Bush denounced the claim — contained in the human rights group’s annual report — as an “absurd allegation” based on accounts by detainees “who hate America” and were not telling the truth. The top guns in his administration joined in the counter-attack: Donald Rumsfeld, the defence secretary, said it was inexcusable to compare the prison to Stalin’s vast system of prison camps.

Dick Cheney, the vice- president, accused former inmates of Guantanamo of “peddling lies”, while General Richard Myers, chairman of the joint chiefs of staff, called the allegations “absolutely irresponsible”.

The criticism of Amnesty intensified when it emerged that William Schultz, the director of Amnesty’s American branch, donated the maximum permissible $2,000 (£1,100) to the campaign of John Kerry, the Democrat candidate, in last year’s presidential race.

A spokesman at Amnesty’s British headquarters said there was no rule forbidding political donations. “We’ve taken the opportunity to criticise all governments on human rights,” he said. “Nobody can point to our work and say it’s been partisan.”

Condoleezza Rice, the secretary of state, admitted at a recent private meeting that the perception of abuse at Guantanamo Bay was becoming a serious problem for the administration.

Explore World News

• Iraq News

• US & Americas News

• Europe News

• Middle East News

• Asia News

• Africa News

• Ireland News

Times Recommends

• Afghanistan: A country locked in a spiral of doom
• Liberal challenges prohibitionist Islam
• Flying yacht in battle to crack 50-knot barrier