However, Brigadier General Jay Hood, who led the inquiry into allegations, denies there is any evidence to support Newsweek's original story in May that a copy of the Qur'an had been flushed down the toilet.
The admission relates to 'lesser' abuses such as standing on the Qur'an during an interrogation, 'inadvertently' spraying urine on the book and getting copies wet.
The admission is hardly a surprise. Since White House spokesperson Scott McClellan's outright condemnation of Newsweek and his claim that the magazine 'had got the facts wrong', there has been a creeping realisation in political and media circles that while the specifics of the case may be unproven, the substance of the claim that abuses had taken place was indeed correct.
So much so that in hindsight, the Pentagon's condemnation of the article as inflammatory - and ostensibly to blame for 16 deaths and over 100 injuries in riots in Afghanistan, Pakistan, India and Indonesia - now looks like a monumental piece of buck-passing.
So should Newsweek have bowed to Pentagon pressure and published its retraction, believing the substance of what it reported was true, or could the editor have been stronger? And was the US administration - as McClellan believes - within its rights to interfere in such a heavy-handed way with the media?
Alastair Campbell's feud with the BBC aside, in the UK we have a voluntary agreement called the DA notice system, created by civil servants and editors, which encourages restraint on the publication of matters such as military plans, nuclear installations and details of intelligence services.
DA notices do not routinely cover the more subtle and complex sensitivities that are arising from a new kind of long-running war on terror - alleged abuse of the Qur'an, or information on how to create ricin, for example - and questions of whether editors should take the line of 'publish and be damned'.
As this new kind of war evolves, opportunities to offend or to breed terrorism can only increase. The freedom enjoyed by the press in Britain is one of our greatest achievements and must be defended, but editors are likely to find themselves battling with far thornier ethical dilemmas than those posed by recent spats over celebrity privacy.