Early January 2002. The Taliban regime in Kabul had been toppled, Nato forces were spreading out across Afghanistan, and the initial military response to the events of September 11 appeared to be running smoothly.

But in Whitehall – and particularly at the Foreign Office – there were the first signs of nervousness over the proposed manner of dealing with one problem that had arisen in the country: a small number of British citizens and residents, all Muslims, had been detained by US forces.

A mass of documents disclosed during high court proceedings show how rapidly the government became involved in the abduction and torture of these individuals in its attempts to secure the UK against attack by al-Qaida.

They also appear to show how little regard was given within the government to the illegality of its own actions.

On 4 January 2002, a memo circulated to the secretaries of the junior Foreign Office ministers Ben Bradshaw and Lady Amos, as well as to the Foreign Office press office and the department's senior legal adviser, Sir Michael Wood, notes: "Public opinion has on the whole shown little concern about the welfare of the British detainees, or the legal terms of their detention. But the issue is clearly of sensitivity to Muslim opinion in the UK and abroad."

It adds that the FCO should be "seen as applying our normal standards of consular assistance as far as possible". Consular officials had not seen these detainees, however, and "our holding line, that we are first seeking to establish identity details, is wearing thin", not least because extensive reports about one individual had already appeared in the press.

At this time, the fact that "rendition" – abducting an individual and moving them against their will from one country to another – was illegal appears not to have been a concern. A document disclosed by the Foreign Office, dated 10 January 2002 and entitled Afghanistan UK Detainees, expresses the government's "preferred options". It states: "Transfer of United Kingdom nationals held by US forces in Afghanistan to a United States base in Guantánamo is the best way to meet our counter-terrorism objectives, to ensure they are securely held." The "only alternative", the document adds, would be to place these individuals in the custody of British forces in Afghanistan, or to return them to the UK.

At around the same time Jack Straw, then foreign secretary, was sending a telegram to several British diplomatic missions around the world in which he signalled his agreement with this policy, but made clear that he did not wish to see the British nationals moved from Afghanistan before they could be interrogated.

"A specialist team is currently in Afghanistan seeking to interview any detainees with a UK connection to obtain information on their terrorist activities and connections," Straw wrote.

"We therefore hope that all those detainees they wish to interview will remain in Afghanistan and will not be among the first groups to be transferred to Guantánamo. A week's delay should suffice. UK nationals should be transferred as soon as possible thereafter."

In the event, the "interview" process in Afghanistan took considerably longer. The manner in which some were conducted is revealed within the reports that an MI5 officer sent to London after each of his encounters with Omar Deghayes, a Libyan-born British resident who was being held at the US air base at Bagram, north of Kabul, in June and July that year. Deghayes is one of the men currently suing the government.

The MI5 interrogators were clearly aware of the manner in which Deghayes was being mistreated. Their only emotional reaction to his plight appears to have been disgust at his physical condition. Considering him to be insufficiently forthcoming, they decided to abandon him to further treatment at US hands.

Some of the disclosed documents are fragmentary and partially intelligible.

Much to the anger of lawyers representing those men suing the government, a number have been blacked out completely, leaving only a date.

A page of one document bears the MI5 letter head and logo, but has been so heavily redacted that only one word, "conclusion", remains visible. Among the papers is a handwritten note, headed "Warriors 14/1", that appears to relate to the state of a detainee in Afghanistan. It states: "Interview conditions: cold beaten up." According to one of the claimants' lawyers it dates from a period when MI5 officers were interviewing detainees in Kabul. The note appears to end with a list of options which includes "collusive deportation extradition".

There is a clear account of the fate of Martin Mubanga, another of the men suing the government, despite the large amounts of black ink that were used to conceal parts of the documents relating to his case before they were handed over.

A joint Zambian-British citizen, Mubanga travelled after 9/11 from Afghanistan to Zambia, where he was detained in March 2002 by Zambian officials accompanied by Americans. A number of messages between the British high commission in Lusaka and the Foreign Office in London show that Blair's office had decided that "under no circumstances should Mubanga be allowed to return to the UK". Should consular officials obtain access, however, there was a danger that the Zambians would hand Mubanga over to the British.

The exchanges become increasingly irate, with one official complaining about "the schizophrenic way in which policy on this whole case was handled in London": one half of the Foreign Office was insisting that Mubanga was entitled to consular assistance, and the other half was saying it should not take responsibility for him.

It had put the British high commission in Lusaka "in an impossible position", and there was a need for "co-ordinated thinking" to avoid such problems arising in future.

The documents show that there had been a proposal to put Mubanga on trial in the UK, but as a consequence of the British decision to wash their hands of him he was flown to Guantánamo, where he spent the next 33 months.

It was not the only time the prime minister's office intervened to thwart attempts by Foreign Office officials to obtain a degree of protection for British citizens, according to the documents.

Minutes prepared for the Home Office terrorism and protection unit after a meeting in April 2002 of officials including John Gieve, the Home Office permanent under-secretary, state that the American authorities had been informed that the British government might begin making public requests for legal access to British men held at Guantánamo. "FCO had wanted to do this (and wanted to be seen to be doing it) but had been overruled by No 10," the minutes say.

The same minutes show that while consideration was being given to the prosecution in the UK of some individuals in Afghanistan, David Blunkett, home secretary, warned there would be questions about the public interest in prosecuting "young and ill-informed individuals who may have been manipulated by others".

Missing from the documents so far disclosed is a copy of the secret policy that governed MI5 and MI6 officers interrogating detainees held overseas between mid-2004 and earlier this month, when it was revised on the orders of the coalition government.

The court had ordered that it be handed over by last Friday, but it failed to materialise. Instead, lawyers for the six men were given the chapter from MI6's manual that deals with detainee operations. This explains that MI6 officers are involved in detaining suspects or helping others do so; interviewing; and preparing reports based on details passed by overseas agencies.

When detaining suspects themselves, officers should consult superiors and consider where the detainee will be held and how they will be treated. There is another consideration. "Is it clear that detention, rather than killing, is the object of the operation?" the manual asks.

This document was handed over instead of one that is known to be extraordinarily sensitive. Ministers of the last government repeatedly insisted that the secret interrogation policy of recent years should never be made public.

The former foreign secretary David Miliband even indicated to a Commons select committee that to do so would "give succour" to the nation's enemies.

Redactions

The black ink that obscures parts of Security Service and Foreign Office papers has frustrated lawyers for the six claimants. Known as redactions, the boxes hide information deemed too sensitive to release on national security grounds. Sapna Malik, representing Binyam Mohamed, complains that they make it hard to reach a settlement and avoid protracted litigation. Any assessment is made "very difficult by the limited nature of the disclosure provided to date, the heavy redaction of the handful of potentially relevant documents … and the refusal of the [government] to provide meaningful answers to the claimants' requests for further information".

Nonetheless, despite so much being withheld, the release of security service reports of interviews with detainees in Guantánamo Bay and other overseas detention centres is almost unprecedented.