Soldiers have described beatings, psychological torture and other physical mistreatment at a camp near Baghdad where General Stanley McChrystal, then commander of US Joint Special Operations forces in Iraq, was frequently seen.
A tall Irish-American with a deceptively gentle manner, Gen McChrystal was named last week as the next head of Afghan operations. He is currently operations director for the US Joint Chiefs of Staff.
The investigation into human rights abuses was led by Marc Garlasco, himself a former Pentagon intelligence officer who helped lead the hunt for former Iraqi dictator Saddam Hussein. Now a weapons expert at Human Rights Watch, his report, No Blood No Foul, covered the period 2003-2004 when Gen McChrystal operated in the shadows and hunted insurgents across Iraq.
Gen McChrystal is likely to be questioned over the findings of the report, compiled in 2006, during Senate hearings which are needed to confirm his appointment to his new post.
His special operations unit used Camp Nama, an acronym for "Nasty Ass Military Area", which had a fearsome reputation.
According to Mr Garlasco's report, which was based on soldiers' evidence, inmates at the camp were regularly stripped naked, subjected to sleep deprivation and extreme cold, placed in painful stress positions, and beaten. Gen McChrystal is lionised in the US as a warrior-scholar. Last week the media has carried admiring reports on how he eats just one meal a day and operates on a few hours' sleep. He led Task Force 121, the Special Operations units in Iraq which caught Saddam Hussein and killed Abu Musab al-Zarqawi, the leader of al-Qaeda in Iraq.
His appointment signals a dramatic shift in US tactics, from reaching out to the Taliban in favour of a more aggressive military approach. But critics warn that Gen McChrystal's robust methods may generate more hostility among Afghan civilians to US and other Nato forces. Roger Carstens of the Center for a New American Security, himself a former special forces officer, said: "Has he ever worked in the counterinsurgency environment? Not really."
One senior official who asked for the identity of the respected international organisation for which he works to be withheld said: "Expect to see secret, dead of night raids in Afghanistan, with more civilians getting hurt and no one being held accountable. It's a big tactical shift. Because of his history in Iraq we were very alarmed when we heard he was going to be in charge in Afghanistan."
Mr Garlasco said that, as the top commander, Gen McChrystal "can allow the special forces to operate with impunity, or he can rein them in and use counterinsurgency tactics like (General David) Petraeus."
Mr Garlasco interviewed a special forces soldier named Jeff who accused Gen McChrystal of banning the Red Cross and other investigators from entering Camp Nama, a decision which was viewed as a violation of the Geneva Conventions.
"Once, somebody brought it up with the colonel," reported the soldier. "'Will [the Red Cross] ever be allowed in here?' And he said, 'Absolutely not.' He had this directly from General McChrystal and the Pentagon that there's no way that the Red Cross could get in. 'They won't have access and they never will.'"
"This facility was completely closed off to anybody investigating, even to Army investigators."
A spokesman for Gen McChrystal said last night it would be "inappropriate" to comment on the details of the Human Rights Watch report or a subsequent investigation by Esquire magazine. The Pentagon also refused to discuss the operations run by Gen McChrystal at the time, saying it "might lead to unravelling of state secrets that have been so beneficial in Iraq."
In another brush with controversy, General McChrystal was blamed for helping to fabricate false information in the drama surrounding the death in 2004 of Pat Tillman, a professional football player who volunteered for the army only to be killed by friendly fire in Afghanistan.
Gen McChrystal approved paperwork recommending Tillman for a silver star which stated that he died from "devastating enemy fire", and backtracked only when he learned that President George W Bush was about to quote from the citation in a speech. The US Army overruled a Pentagon recommendation that he be held accountable for his actions.
Last week the Tillman family attacked Gen McChrystal's new appointment. The dead soldier's mother, Mary Tillman, said, "It is imperative that Lt Gen McChrystal be scrutinised carefully during the Senate hearings."