When the details of Abu Ghraib broke, the CIA was implicated by those involved the in the abuse and torture. They -- to a man and woman -- said their "orders" to conduct these abuses came from above, the actions they were directed to "apply" to the prisoners were detailed by the CIA, and they were supervised by the CIA. In the photos of the abuse at Abu Ghraib, you can see persons not in military uniforms, but civilian clothes.

From Wikipedia:

"The United States Department of Defense removed seventeen soldiers and officers from duty, and seven soldiers were charged with dereliction of duty, maltreatment, aggravated assault and battery. Between May 2004 and September 2005, seven soldiers were convicted in courts martial, sentenced to federal prison, and dishonorably discharged from service. Two soldiers, Specialist Charles Graner, and his former fiancee, Specialist Lynndie England, were sentenced to ten years and three years in prison, respectively, in trials ending on January 14, 2005 and September 26, 2005. The commanding officer at the prison, Brigadier General Janis Karpinski, was demoted to the rank of Colonel on May 5, 2005. Col. Karpinski has denied knowledge of the abuses, claiming that the interrogations were authorized by her superiors and performed by subcontractors, and that she was not even allowed entry into the interrogation rooms.

On December 21, 2004, the American Civil Liberties Union released copies of FBI internal memos they had obtained under the Freedom of Information Act concerning alleged torture and abuse at Guantanamo Bay, in Afghanistan and in Iraq. One memo dated May 22, 2004 was from someone whose name was blanked out but was described in the memo as "On Scene Commander "Baghdad".[83] He referred explicitly to an Executive Order that sanctioned the use of extraordinary interrogation tactics by U.S. military personnel. The methods explicitly mentioned as being sanctioned are sleep deprivation, hooding prisoners, playing loud music, removing all detainees' clothing, forcing them to stand in so-called "stress positions", and the use of dogs. The author also claimed that the Pentagon had limited use of the techniques by requiring specific authorization from the chain of command. The author identifies "physical beatings, sexual humiliation or touching" as being outside the Executive Order. This was the first internal evidence since the Abu Ghraib prisoner abuse affair became public in April 2004 that forms of abusive coercion and torture of captives had been mandated by the President of the United States.[84]

The Final Report of the Independent Panel to Review DoD Detention Operations did specifically absolve senior U.S. military and political leadership from direct culpability: