A senior Bush administration official and former head of the 9/11 Commission has described CIA interrogation techniques used on alleged terrorists as torture and said he warned in a secret memo at the height of the "war on terror" that they breached the US's own war crimes laws.

Philip Zelikow, who was the US secretary of state Condoleezza Rice's most senior official, told the Guardian that he now regards what officials euphemistically called "enhanced interrogation", such as sleep deprivation and waterboarding, as torture – although he did not use that word at the time and is reluctant to use it now.

Zelikow, whose official position was counsellor to Rice, said he had her support on the issue. As the state department's representative on the National Security Council committee considering legal issues around violent interrogations, he expressed his concerns at the time in a top secret 2006 memorandum.

The memo, to other members of the committee who represented the justice and defence departments and intelligence services, warned that the CIA's use of waterboarding and other abuses were almost certainly in breach of US and international law. But the memo so alarmed the administration that it was immediately rejected and all copies were ordered destroyed.

A draft version of the memo, found at the state department, was released this week following a freedom of information request by the National Security Archive in Washington.

Zelikow told the Guardian in an email exchange that while he did not use the word torture in the memo, he believes that is what the CIA was using. "I do regard the interrogation practices and conditions of confinement, taken together, as torture – in the ordinary layman's use of this term. But … 'torture' is also a term with a carefully worded legal meaning and definition. So I tend to avoid talking about 'torture' because it would appear I'm accusing officials of criminal activity, which I'm not sure was the case," he said.

"I have sometimes just referred to 'physical torment' instead, which seems expressive and is accurate."

Zelikow said he is uncertain whether individuals in the CIA or other services are guilty of war crimes or have other criminal liability over the use of torture because they were told by the office of legal counsel, which provides legal advice to the president, that techniques such waterboarding, which causes the sensation of drowning, sleep deprivation and stress positions, were legal.

"For better or worse, but mainly better, to be a crime one must violate the law. To be an intentional crime … So the attorney general's legal position telling officials their conduct is legal really did matter," he said. "Had I been in the attorney general's or OLC's position in 2002, I would not have interpreted either the war crimes statute (as written then) or the torture statute in the way those officials interpreted them. But they made their choices and had the authority to make them."

But he said he has little doubt that the methods were unacceptable. "I think what they did was wrong," he said.

Zelikow said that a later supreme court ruling that the Geneva Conventions do apply to those deemed by the Bush administration to be "illegal combatants" reinforced his position that some of the CIA's interrogation methods were illegal. "If I was right, officials would be violating the federal War Crimes Act, a felony punishable by up to life imprisonment," he told the Guardian.

Among those subjected to waterboarding and other tortures was the alleged mastermind of the 9/11 attacks, Khalid Sheikh Mohammed, who is expected to go on trial for his life in the coming months along with four suspected co-conspirators at a Guantánamo military tribunal.

In his 2006 memorandum to other members of the National Security Council committee of deputies to cabinet secretaries, the highest level interagency committee considering the legality of "enhanced interrogations", Zelikow said that such methods were in breach of the Convention Against Torture as well as a recent US law that "extended the prohibition against cruel, inhuman or degrading treatment to all conduct worldwide".

Zelikow argued that US law on the issue applied the American constitution's own standard regarding "cruel and unusual punishment" and that there is a long history of case law that prevents techniques used by the CIA from use in the US.

"The techniques least likely to be sustained are the techniques described as "coercive", especially viewed cumulatively, such as the waterboard, walling, dousing, stress positions and cramped confinement," Zelikow wrote in the memo. "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, even where the prisoners were presumed to be unlawful combatants."

Toward the end of the memo, part of a section has been blacked out by a censor. It refers to foreign governments abandoning several of the techniques Zelikow criticises. Asked if those governments include the UK, he said: "Yes."

Zelikow said his position as counselor to Rice did not entitle him to offer a legal opinion, but he felt obliged to put an alternative view before his colleagues at other agencies to warn them that the courts may take a different view.

Asked if Rice knew of and approved his memo, Zelikow said: "I kept her fully informed on what I was doing. She supported my work."

Zelikow said that after the office of legal counsel decided his memorandum "was not appropriate for further discussion", the order came from the White House to destroy all copies. "I don't know who suggested this or why. I ignored the suggestion since it seemed so obviously improper," he said.

The existence of the memo came to light when Zelikow gave testimony to the Senate judiciary committee two years ago in which he described the systematic physical abuses by the CIA as "unprecedented" and said that at least some of the legal opinions of justice department lawyers on the maltreatment of prisoners were "unsound, even unreasonable".

"The US government adopted an unprecedented programme of coolly calculated dehumanising abuse and physical torment to extract information. This was a mistake, perhaps a disastrous one," he said.

Zelikow said he became concerned while serving as executive director of the 9/11 Commission, which investigated the circumstances of the terrorist attacks, because of the CIA's unwillingness to disclose information about the interrogation of detainees and its refusal to permit access to them.

The commission made a recommendation that captured prisoners, even if defined as illegal combatants, should be treated to a standard that fits with the Geneva Conventions. The Bush administration rejected it. He finally discovered the details of the CIA programme when he was appointed to the NSC committee.

Zelikow said the policy was shaped in an "understandably merciless" atmosphere after the 9/11 attacks. "The feeling of being at war was real, at least in the White House. Almost every morning, President Bush himself received nerve-jangling briefings just on the latest threats," he told the Senate.

Zelikow described an atmosphere in which policymakers fell under the spell of the intelligence community and became deferential "in a time of seemingly endless alarms". But, he added, the CIA had no real experience of interrogating enemy captives and so "improvised an unprecedented elaborate, systematic programme of medically monitored physical torment to break prisoners and make them talk".

"The intelligence community's position in 2005, and later, was that a substantial programme of intense physical coercion was uniquely necessary to protect the nation," he said.

But Zelkow said there were other, more established means of interrogation well known to law enforcement and the military.

"The point is not whether the CIA programme produced useful intelligence. Of course it did. Quite a lot. The CIA had exclusive custody of a number of the most important al-Qaeda captives in the world, for years. Any good interrogation effort would produce an important flow of information from these captives," he said.