A 14 September 2003 memo signed by Lieutenant-General Ricardo Sanchez authorised 29 methods of interrogation, including 12 which "far exceeded" US military regulations as well as the Geneva Conventions covering prisoners of war, the ACLU said.
The methods included using muzzled army dogs in a way that "exploits Arab fear of dogs", and placing detainees in painful "stress positions".
The memo also authorised techniques of isolation and sleep and food deprivation and sensory manipulation to break down prisoners.
"General Sanchez authorised interrogation techniques that were in clear violation of the Geneva Conventions and the army's own standards," ACLU lawyer Amrit Singh said in a statement.
Singh called for Sanchez and other high-ranking US officials responsible for alleged prisoner abuse in Iraq to be held accountable.
"General Sanchez authorised interrogation techniques that were in clear violation of the Geneva Conventions and the army's own standards"
American Civil Liberties Union lawyer
Sanchez stepped down from his job of leading US forces in Iraq in July 2004 following revelations of torture in Baghdad's Abu Ghraib prison.
The Sanchez memo's existence had been known for some time, but it was only obtained by the ACLU from the Defence Department on Friday following multiple court-supported requests. The department had refused to release the memo on national security grounds.
Rejecting suggestions that the memo's release was stalled to avoid embarrassment, Defence Secretary Donald Rumsfeld insisted on Tuesday that the department maintains "full transparency", mitigated only by the demands of national security.
Earlier in March, the ACLU and Human Rights First filed a lawsuit asserting Rumsfeld had direct responsibility for the torture and abuse of prisoners held by the US in Iraq, Cuba, Afghanistan and elsewhere.
The ACLU has filed similar suits charging Sanchez and other US generals with responsibility for abuse of detainees.
In an unrelated development, another US rights group - Human Rights Watch - has also released a report concerning a Yemeni intelligence officer who was kidnapped by Egyptian authorities in Cairo in 2002.
He was then sent to US jails in Afghanistan and Cuba entirely outside the rule of law, HRW said on Tuesday.
The watchdog called the case of Abd al-Salam Ali al-Hila a "reverse rendition", a twist on the US government practice of rendering certain prisoners to third nations for interrogation and, in the view of rights activists, torture.
Al-Hila was the latest of about 10 known cases of men seized by other countries not on a battlefield and handed over to the US for indefinite detention as an "enemy combatant" without legal process, according to HRW military affairs researcher John Sifton.
"One thing that we're trying to point to here is the way in which these reverse renditions occur entirely outside the rule of law," Sifton said. There had been no extradition process, no criminal suspicion based on probable cause, and no ability to challenge the detention, he said.
"These renditions result in people disappearing," Sifton added. "Is this man dangerous? Perhaps. But the point is he should be given an opportunity to challenge his detention."