A letter written by lawyers for Binyam Mohamed and sent to the Intelligence and Security Committee (ISC) detailed a number of "inaccuracies" in the MPs' report on the UK's alleged involvement in rendition.
It made clear that evidence given to the High Court about what the secret services knew of Mr Mohamed's treatment by the CIA was in stark contrast with the committee's findings, which exonerated MI5 of collusion in torture.
Writing in August last year Mr Mohamed's lawyer, Clive Stafford Smith, drew the MPs' attention to evidence showing that MI5 officers must have known that Mr Mohamed was being unlawfully held and ill-treated when they gave evidence.
This week, three Court of Appeal judges ruled in favour of publishing a summary of this evidence, which they said showed Mr Mohamed, 31, had been denied sleep and threatened with "disappearance". The judges said MI5 would have known about this treatment but continued to co-operate with the CIA in Mr Mohamed's interrogation in Pakistan in 2002.
Next week they will decide whether to publish their full judgement, which is believed to make direct criticism of MI5 and its "culture of suppression".
In August last year, Mr Stafford Smith wrote to the MPs saying: "New documents belatedly supplied by the Secret Intelligence Services to the court expose a number of factual inaccuracies in the ISC's report. I stress that these errors are not the fault of the ISC, but are occasioned by the false testimony that the ISC received (which was apparently similar, I am sad to say, to the false and incomplete testimony given before the High Court)."
But yesterday the chairman of the ISC denied that his committee had been misled by MI5. In an interview with BBC Radio 4's Today programme, Dr Kim Howells said any claim that the intelligence services were colluding in torture was "a calumny and a slur and should not be made".
He also appeared to attack the senior judge in the Binyam Mohamed ruling, Lord Justice Neuberger: "I don't know what the Master of the Rolls is doing or playing at. He sometimes chooses to put some information in his reports and he says he sometimes doesn't. The role of the judiciary is something that I can't account for. That's something they have to defend."
Dr Howells added: "[I am telling you] that our completely independent investigations don't seem to confirm that the agencies are involved in any way in torture or complicity in torture."
He said his view was underpinned by a conversation he had with the head of MI5, Jonathan Evans, who assured him MI5 had not been involved. In a rare public intervention, Mr Evans said criticism of the security service could help Britain's enemies. They would use "propaganda and campaigns to undermine our will and ability to confront them", he wrote in the Daily Telegraph. "We would do well to maintain a fair and balanced view of events ... and avoid falling into conspiracy theory and caricature," he said.
The intelligence and security services say they have passed on any documents to the relevant authorities as they have come to light. These include papers which directly led to two separate Scotland Yard investigations, one into the Binyam Mohamed affair and a separate one into handing over prisoners to the Americans in Iraq.
The documents – which were found, it is claimed, in a collection of material held by MI6 – were passed on to the Attorney General, who ordered the police investigations.
A 2007 report by the ISC stated that an MI5 agent, "Witness B", had visited Mr Mohamed in Pakistan in 2002 but has had no further contact with the agency. But Mr Mohamed's lawyers say that documents subsequently presented to the High Court by MI6 show that US authorities continued to supply information to Britain from him until 2004.
Binyam Mohamed: The facts, the allegations and the political reaction
Q. Who is Binyam Mohamed and what happened to him?
A. Binyam Mohamed al-Habashi, an Ethiopian national, sought asylum in the UK in 1994. He was given indefinite leave to remain and in June 2001 he travelled to Afghanistan, where he is said to have fought alongside the Taliban. He has since described the Taliban as the "best government Afghanistan has had in 20 years". Pakistani authorities arrested Mr Mohamed and, he claims, he was deprived of sleep during interrogation in Karachi. He was subsequently sent to Morocco where, he says, he was subjected to torture, before being moved to Guantanamo Bay. He was released and returned to Britain last year.
Q. What lies behind the current controversy over the role of British intelligence in the alleged torture of Binyam Mohamed?
A. The Foreign Secretary David Miliband had taken legal action to keep secret seven paragraphs of "sensitive information" about Mr Mohamed being mistreated while in American custody. A draft judgment by the Master of the Rolls, Lord Neuberger, was sent to the parties involved in the action. Jonathan Sumption QC, acting for the Government, maintained to the court that the draft judgment was portraying MI5 as not respecting human rights; having a "culture of suppression"; not renouncing "coercive interrogation"; and deliberately misleading MPs in the Commons Intelligence and Security Committee (ISC). Mr Miliband lost the case.
Q. What will now happen to the judgment?
A. Lord Neuberger and his two fellow Appeal Court judges have stated that they have accepted Mr Sumption's argument, but they have been asked by Mr Mohamed's lawyers, and those of a number of media organisations, to reconsider this acceptance.
Q. What has been the reaction of MI5, Government and the ISC?
A. The head of MI5, Jonathan Evans, says that the claims in the draft judgment were "the precise opposite of the truth". The Home Secretary, Alan Johnson, has described the media coverage of the affair as "baseless, groundless accusations" and "ludicrous lies". Mr Miliband also strongly defended the security and intelligence services. Kim Howells, chairman of the ISC, has denied that the committee was misled by MI5.
Q. What has been the reaction of the opposition parties?
A. The Liberal Democrat leader, Nick Clegg, has claimed that ministers "at the very top of the Government" knew Britain was potentially complicit in torture but failed to act. David Davis, the former shadow Home Secretary and now a backbench Conservative MP, accused MI5 and MI6 of complicity in torture, adding that the alleged mistreatment of Mr Mohamed "seems like something the Gestapo got up to".
Q. How much did British intelligence and security services know about Mr Mohamed's mistreatment?
A. An MI5 officer, "Witness B", travelled to Karachi in Pakistan in 2002. He said he observed no abuse and Mr Mohamed did not complain to him about abuse. According to the evidence given to the ISC by MI5, they had no further contact with the prisoner. But the then-director general of MI5, Dame Eliza Manningham-Buller, told the ISC that "with hindsight" she regretted not seeking assurance from the Americans that Mr Mohamed would not be abused.
Mr Mohamed's lawyers, Reprieve, claim that intelligence documents presented to the High Court showed that the US continued to supply information from Mr Mohamed to the UK until March 2004.
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