Secret CIA video tapes of the waterboarding of Osama Bin Laden's suspected jihadist travel arranger Abu Zubaydah show him vomiting and screaming, the BBC has learned.
The tapes were destroyed by the head of the CIA's Counterterrorism Center, Jose Rodriguez.
In an exclusive interview for Newsnight, Rodriguez has defended the destruction of the tapes and denied waterboarding and other interrogation techniques amount to torture.
The CIA tapes are likely to become central to the trial of Khalid Sheikh Mohammed, the alleged mastermind of 9/11, at Guantanamo Bay.
When Khalid Sheikh Mohammed appeared before a special military tribunal at Guantanamo Bay last Saturday, he refused to put on the headphones that would enable him to hear the translator.
His civilian attorney, David Nevin, said he could not wear them because of the torture he had suffered during his interrogation.
His "torture" at the hands of his CIA interrogators at a secret "black site" to which he had been rendered, included being deprived of sleep for over a week, standing naked, wearing only a nappy, and being waterboarded 183 times.
The CIA and the US Department of Justice that authorised the secret interrogation programme in the wake of 9/11, euphemistically referred to its content as "enhanced interrogation techniques".
Most people would probably call them "torture", but Jose Rodriguez disputes this term.
He has written a book, "Hard Measures" in which he defends the use of such techniques, and he told me there is no doubt they were effective.
"Khalid Sheikh Mohammed was probably the toughest detainee that we ever had and he was going to resist to the end of his strengths," he told me.
Waterboarding is simulated drowning. The detainee is stripped naked and strapped onto a board in a horizontal position with feet higher than his head.
Water is then dripped onto a cloth covering the nose and mouth which makes the detainee choke and temporarily stop breathing.
"It's not a pretty sight when you are waterboarding anybody or using any of these techniques, let's be perfectly honest," Rodriguez admitted.
Only three of the CIA's "high value targets" were waterboarded.
Abd al-Rahim al-Nashiri, the alleged architect of the 2000 attack on the USS Cole in which 17 sailors died, was waterboarded twice, and Abu Zubaydah, Osama Bin Laden's suspected travel agent for jihadis, 83 times.
And it is the waterboarding of Zubaydah that has now become the centre of fresh controversy triggered by Newsnight's investigation.
The CIA recorded Zubaydah's detention and interrogation - and that of other detainees - on 92 video tapes.
Twelve of them covered the application of the "enhanced interrogation techniques", including waterboarding.
On one or more of them, I understand Zubaydah is shown vomiting and screaming.
John Rizzo, the CIA's top legal counsel who oversaw the legalisation of the techniques in an exchange of memoranda with the Department of Justice, wanted to be certain that what was happening at the black site was in accordance with what had been legally agreed.
He had not anticipated that waterboarding would be used as often as it was. And he sent one of his most experienced colleagues to the black site, believed to be in Thailand, to find out.
Rizzo's colleague viewed all the 92 hours of video and concluded that the techniques were being legally applied, but he was uncomfortable about what he saw.
"He did say that portions of the tapes, particularly those of Zubaydah being waterboarded, were extraordinarily hard to watch," Rizzo told me.
"He [Zubaydah] was reacting visibly in a very disturbing way."
So was he being sick?
"He was experiencing some physical difficulties, I'll just leave it at that... 'tough to watch in places' was his term."
I asked Jose Rodriguez if he had seen the tapes. He said he had not. Was he aware that they showed Abu Zubaydah vomiting and screaming? He said he was not. He checked with his interrogators at the black site who said there was no vomiting or screaming.
"I don't know where you got that from", he said. "I don't know about screaming and vomiting but it's not a pretty sight."
Rodriguez knew the tapes were potentially a ticking time bomb and wanted to destroy them. He waited for three years with increasing exasperation at the apparent unwillingness of anybody on high to take responsibility for authorising their destruction.
Then when news of the CIA's secret black sites leaked, Rodriguez's patience ran out.
Believing he had the authority to do so, he ordered the 92 tapes to be minced in an industrial shredder.
"Our lawyers said it was legal," he said.
But Rizzo was not happy.
"I was stunned and angry and honestly a bit hurt. I made it clear to him, as did two CIA directors, that he did not have the authority to make a decision to destroy those tapes."
So I asked, "He disobeyed orders?"
But Rodriguez is adamant that he acted legally and says his motive in ordering their destruction was to protect the identities of his CIA interrogators lest they suffer reprisals.
But there was more to it than that. Three days after the tapes had been shredded, a CIA memorandum, since released under America's Freedom of Information Act, reported comments by Jose Rodriguez:
"As Jose said, the heat from destroying [the tapes] is nothing compared to what it would be if the tapes got into the public domain - he said that out of context they would make us look terrible - it would be devastating to us. All in the room agreed."
I put this to Rodriguez and he was typically upfront about it.
"I said that, yes. If you're waterboarding somebody and they're naked, of course that was a concern of mine."
Despite all the controversies around the CIA's black sites and its interrogation programme, Jose Rodriguez stands by all that he did.
"I was honoured to serve my country after the 9/11 attacks. I am proud of the decisions that I took including the destruction of the tapes to protect the people who worked for me. I have no regrets."
No doubt defence lawyers at Khalid Sheikh Mohammed's trial will try and get access to the written records that exist of what was on the tapes and seek to question the CIA lawyer who viewed them.
But under the rules of the military tribunal that restrict any discussion of torture, they are unlikely to succeed.
Watch Peter Taylor's full interview with Jose Rodriguez on Newsnight on Wednesday 9 April 2012 at 22:30 BST on BBC Two.