A top adviser to former Secretary of State Condoleezza Rice warned the Bush administration that its use of “cruel, inhuman or degrading” interrogation techniques like waterboarding were “a felony war crime.”

What’s more, newly obtained documents reveal that State Department counselor Philip Zelikow told the Bush team in 2006 that using the controversial interrogation techniques were “prohibited” under U.S. law — “even if there is a compelling state interest asserted to justify them.”

Zelikow argued that the Geneva conventions applied to al-Qaida — a position neither the Justice Department nor the White House shared at the time. That made waterboarding and the like a violation of the War Crimes statute and a “felony,” Zelikow tells Danger Room. Asked explicitly if he believed the use of those interrogation techniques were a war crime, Zelikow replied, “Yes.”

Zelikow first revealed the existence of his secret memo, dated Feb. 15, 2006, in an April 2009 blog post, shortly after the Obama administration disclosed many of its predecessor’s legal opinions blessing torture. He briefly described it (.pdf) in a contentious Senate hearing shortly thereafter, revealing then that “I later heard the memo was not considered appropriate for further discussion and that copies of my memo should be collected and destroyed.”

At least one copy survived in the files of the department’s Bureau of Intelligence and Research. The State Department has now disclosed it to Danger Room, mostly without redactions — three years after this reporter filed an official request for it. You can read the memo for yourself, below.

Zelikow’s memo was an internal bureaucratic push against an attempt by the Justice Department to flout long-standing legal restrictions against torture. In 2005, he wrote, both the Justice and State Departments had decided that international prohibitions against “acts of cruel, inhuman, or degrading treatment or punishment which do not amount to torture” do not “apply to CIA interrogations in foreign countries.” Those techniques included contorting a detainee’s body in painful positions, slamming a detainee’s head against a wall, restricting a detainee’s caloric intake, and waterboarding.

Zelikow wrote that a law passed that year by Congress, restricting interrogation techniques, meant the “situation has now changed.” Both legally and as a matter of policy, he advised, administration officials were endangering both CIA interrogators and the reputation of the United States by engaging in extreme interrogations — even those that stop short of torture.

“We are unaware of any precedent in World War II, the Korean War, the Vietnam War, or any subsequent conflict for authorized, systematic interrogation practices similar to those in question here,” Zelikow wrote, “even where the prisoners were presumed to be unlawful combatants.”

Other “advanced governments that face potentially catastrophic terrorist dangers” have “abandoned several of the techniques in question here,” Zelikow’s memo writes. The State Department blacked out a section of text that apparently listed those governments.

“Coercive” interrogation methods “least likely to be sustained” by judges were “the waterboard, walling, dousing, stress positions, and cramped confinement,” Zelikow advised, “especially [when] viewed cumulatively.” (Most CIA torture regimens made use of multiple torture techniques.) “Those most likely to be sustained are the basic detention conditions and, in context, the corrective techniques, such as slaps.”

Zelikow’s warnings about the legal dangers of torture went unheeded — not just by the Bush administration, which ignored them, but, ironically, by the Obama administration, which effectively refuted them. In June, the Justice Department concluded an extensive inquiry into CIA torture by dropping potential charges against agency interrogators in 99 out of 101 cases of detainee abuse. That inquiry did not examine criminal complicity for senior Bush administration officials who designed the torture regimen and ordered agency interrogators to implement it.

“I don’t know why Mr. Durham came to the conclusions he did,” Zelikow says, referring to the Justice Department special prosecutor for the CIA torture inquiry, John Durham. “I’m not impugning them, I just literally don’t know why, because he never published any details about either the factual analysis or legal analysis that led to those conclusions.”

Also beyond the scope of Durham’s inquiry: The international damage to the U.S. reputation caused by the post-9/11 embrace of “cruel, inhuman and degrading” interrogation methods; and the damage done to international protocols against torture.

Update, 12:15 p.m.: This post has been updated to reflect Danger Room’s interview with Zelikow.