Tony Blair evaded questions over his role in document, and ministers have refused to say if they were aware of details

Government ministers were extraordinarily sensitive about the contents of the secret MI5 and MI6 interrogation policy document when the Guardian became aware of its existence two years ago.

Initially, its purpose was to permit the questioning of prisoners being held at Bagram air base, north of Kabul, in the wake of the 9/11 attacks, despite it being clear that these men were being severely abused by members of the US military.

In time, the policy developed into one governing the conduct of British intelligence officers who were questioning terrorism suspects held by some of the world's most notorious security agencies.

As a number of these men began to emerge from captivity, some bearing clear signs of having been tortured, the ministers became even more nervous. The disclosure of the contents of the document helps explain why.

Tony Blair evaded a series of questions over the role he played in authorising changes to the instructions in 2004, while the former home secretary David Blunkett maintained it was potentially libellous even to ask him questions about the matter.

As foreign secretary, David Miliband told MPs the secret policy could never be made public as "nothing we publish must give succour to our enemies".

Blair, Blunkett and the former foreign secretary Jack Straw also declined to say whether or not they were aware that the instructions had led to a number of people being tortured.

The head of MI5, Jonathan Evans, said that, in the post 9/11 world, his officers would be derelict in their duty if they did not work with intelligence agencies in countries with poor human rights records, while his opposite number at MI6, Sir John Sawers, spoke of the "real, constant, operational dilemmas" involved in such relationships.

Others, however, are questioning whether, in the words of Ken Macdonald, a former director of public prosecutions, "Tony Blair's government was guilty of developing something close to a criminal policy".

The Intelligence and Security Committee, the group of parliamentarians appointed by the prime minister to assist with the oversight of the UK's intelligence agencies, is known to have examined the document while sitting in secret. However, it is unclear what – if any – suggestions or complaints it made.

Paul Murphy, the Labour MP and former minister who chaired the committee in 2006, declined to answer questions about the matter.

A number of men, mostly British Muslims, have complained that they were questioned by MI5 and MI6 officers after being tortured by overseas intelligence officials in Pakistan, Bangladesh, Afghanistan and Guantánamo Bay. Some are known to have been detained at the suggestion of British intelligence officers.

Others say they were tortured in places such as Egypt, Dubai, Morocco and Syria, while being interrogated on the basis of information that could only have been supplied by the UK.

Some were subsequently convicted of serious terrorism offences or subjected to control orders. Others were returned to the UK and, after treatment, resumed their lives.

One is a businessman in Yorkshire, another a software designer living in Berkshire, and a third is a doctor practising on the south coast of England.

Some of the men have brought civil proceedings against the British government, and a number have received compensation in out-of-court settlements. Others remain too frightened to take action.

Scotland Yard has examined the possibility that one officer from MI5 and a second from MI6 committed criminal offences while extracting information from detainees overseas, and detectives are now conducting what is described as a "wider investigation into other potential criminal conduct".

A new set of instructions was drafted after last year's election, published on the orders of David Cameron, on the grounds that the coalition was "determined to resolve the problems of the past" and wished to give "greater clarity about what is and what is not acceptable in the future".

Human rights groups pointed to what they said were serious loopholes that could permit MI5 and MI6 officers to remain involved in the torture of prisoners overseas.

The issue of alleged torture in custody continues to haunt political, military and intelligence elites on both sides of the Atlantic. On Thursday a judge in America allowed a former military contractor who claims he was imprisoned and tortured by the US army in Iraq to sue the former defence secretary Donald Rumsfeld personally for damages.

The man, an army veteran whose identity has been withheld, was working as a translator for the US marines in the volatile Anbar province when he was detained for nine months at Camp Cropper, a US military facility near Baghdad airport dedicated to holding "high-value" detainees.

The US government says he was suspected of helping to pass classified information to the enemy and helping anti-coalition forces enter Iraq. But he was never charged with a crime, and he says he never broke the law.

Lawyers for the man, who is in his 50s, claim he was preparing to return to the US on annual leave when he was detained without justification and that his family were told nothing about his whereabouts or whether he was still alive.

Court papers filed on his behalf say he was repeatedly abused, then released without explanation in August 2006. Two years later, he filed a suit in Washington arguing that Rumsfeld personally approved torturous interrogation techniques on a case-by-case basis and controlled his detention without access to the courts, in violation of his constitutional rights.

Alleged victims

Binyam Mohamed, 33, returned to Britain in 2009 after his release from Guantanámo Bay. An MI5 officer was alleged to have been involved in an interview with Mohamed in Pakistan and to have seen him three times while he was being held in Morocco.

Faisal Mostafa, 47, a chemist from Stockport, was repatriated from Bangladesh last summer after being detained in Dhaka in 2009. He is said to have been hooded, strapped to a chair and questioned about the UK while a drill was driven into his shoulder and hip.

Alam Ghafoor, 40, from Huddersfield, said he was held on a business trip in the United Arab Emirates after the London 7/7 bombings. The Foreign Office insisted he had not been detained at the request of the UK. Released after signing a false confession.

Zeeshan Siddiqui, a British citizen detained by the Pakistani security services and tortured while they accused him of being a member of al-Qaida. He returned to the UK and was placed under a control order. He absconded and is still missing.