The investigation conducted by Brigadier General Richard Formica examined the treatment of Iraqi prisoners following the Abu Ghraib prison scandal in 2004.
The report describes how some detainees were fed nothing but bread and water for up to 17 days by US special operations troops but dismissed allegations that prisoners were physically abused or humiliated at the so-called tactical holding facilities.
The heavily censored report was given to the American Civil Liberties Union under court order as part of a Freedom of Information Act lawsuit.
"The government's own documents demonstrate that the abuse of detainees in Iraq, Guantanamo Bay and Afghanistan was widespread and systemic. It shows that special operations task forces were repeatedly involved in detainee abuse incidents and they continued to escape scrutiny," said Amrit Singh, a lawyer for the civil liberties group.
The report described how special operations troops at a temporary holding facility kept prisoners in a room on a chain about a metre long, with a diet chiefly of bread and water, for up to 17 day. It concluded this was not intended as punishment and that, for short periods, eating just bread and water "is sufficient to maintain good health and prevent the onset of nutritional deficiencies."
"The US policy is to treat all detainees humanely," said Lieutenant Colonel Mark Ballesteros, a Pentagon spokesman.
The report did not recommend that any of the US personnel be disciplined and concluded the incidents were not the result of deliberate or malicious attempts by US forces to abuse detainees.
It called for more training and education in the principles of the Geneva Conventions and greater command oversight. It said that while the treatment of the prisoners was wrong the special operations facilities were inadequate to accommodate detainees.
The inquiry was ordered in May 2004 after the first pictures of US personnel abusing detainees at Abu Ghraib prison were published.
The government also turned over a separate report on the treatment of detainees by US forces in Afghanistan.