British intelligence officers put questions to a man despite knowing he had been subjected to appalling abuse, including being waterboarded 83 times, according to damning evidence contained in a UK parliamentary report published this week.

In the years after 9/11, Abu Zubaydah was the only CIA prisoner who went through all 12 of the agency’s “enhanced interrogation techniques”, including being beaten, deprived of sleep and locked in a small box.

After a four-year inquiry, the all-party intelligence and security committee (ISC) said in its report published on Thursday that MI6 had “direct awareness of extreme mistreatment and possibly torture” of Zubaydah.

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Despite this knowledge, from 2002 to at least 2006, MI6 and MI5 sent questions to be put to Zubaydah, the ISC reported. This was during the period he was being waterboarded and suffering other tortures, the committee noted.

While MI6 may not have known the precise details of the abuse, which resulted in the loss of an eye while in custody, the committee found evidence that one of its senior officers, who had knowledge of the conditions, had noted that “98% of US special forces would have been broken” had they been subjected to the same mistreatment.

In the lead-up to the 2003 invasion of Iraq, statements made by Zubaydah under torture were cited by the US government as evidence that there was a link between the Ba’athist regime of Saddam Hussein and al-Qaida: a connection that was said to justify the invasion of Iraq. That connection is no longer made.

Zubaydah, a Saudi-born Palestinian national who is still being held in Guantánamo Bay, was also said to have confessed that al-Qaida planned to use an improvised nuclear device to attack Washington DC. This too is now accepted to be a false claim.

The ISC report found evidence that UK intelligence officers had been involved in almost 600 cases in which a prisoner was mistreated in the years after 9/11, and that the British government had planned, agreed or financed 31 rendition operations.

Scotland Yard has said it is studying the report, amid warnings that if the UK does not investigate, the international criminal court may do so.

Some MPs are calling for a judge-led inquiry to be convened because Theresa May did not permit the ISC to question low- and middle-ranking intelligence officers, and did not call the then foreign and home secretaries, Jack Straw and David Blunkett.

The committee heard that Scotland Yard had investigated one unproven allegation that a British intelligence officer had beaten a prisoner with a baseball bat. A different MI6 officer reported to London that he had questioned a prisoner at Bagram airbase, in Afghanistan, who had been deprived of sleep for three days and forced into stress positions. “He shook violently from cold, fatigue and fear,” the officer reported, adding that he and the US military “agreed to maintain pressure for the next 24 hours”.

Another MI6 officer had admitted threatening a prisoner with rendition to Guantánamo, saying his wife might be forced to turn to prostitution to feed their children.

When a Foreign Office official heard screams coming from a hangar at Bagram in October 2004, the department agreed to raise the matter with the US government, but there is no record of this having happened.

And when one MI6 officer raised concerns that prisoners at a detention facility were being kept in cells approximately 2 metres long, 1.8 metres high and 1.2 metres wide, he felt he was regarded as having “let the side down” by pointing to an “inconvenient” truth. An MI6 lawyer who visited this facility described it as “a torture centre” in which prisoners were held in wooden crates, could neither stand nor lie and subjected to white noise. The location of this US facility is not identified in the report, but it is thought to have been at Balad airbase, north of Baghdad in Iraq.

MI6 lawyers eventually formulated a policy under which nobody captured by UK forces was sent to this facility and officers would not interrogate anyone sent there. In practice, the report said, they would interrogate prisoners in a Portakabin next door to the prison, to which they would be returned once the questioning was complete.

One MI6 officer is said to have submitted questions to prisoners whom she knew were being starved, dehydrated, deprived of sleep and mistreated somehow through the use of menstrual blood. Another had suggested that prisoners should be forced to parade around their cells with 14kg (30lbs) weights around their necks while being bombarded with rock music and strobe lights, but was overruled by his superiors.

The shocking details buried in the report, which have hitherto not been highlighted, will intensify calls for a public inquiry into the actions of Britain’s security and intelligence services overseas.

The shadow attorney general, Shami Chakrabarti, and the Conservative MP Ken Clarke, who chairs the all-party parliamentary group on extraordinary rendition, have called for an independent judge-led inquiry into the UK’s involvement in detainee mistreatment and rendition.

“These are not small issues which can now be swept under the carpet – and the government must address them urgently,” Clarke said.

However, experts have questioned whether the true picture of what happened will ever emerge.

“The UK has always been reluctant to reveal liaison arrangements with other countries as this could prejudice further arrangements,” said Dr Dan Lomas, an expert in intelligence and security studies at the University of Salford. “Observers shouldn’t get their hopes up about many more details coming out. Nevertheless, this is an issue that will not lie down.”