The true extent of the Labour government's involvement in the illegal abduction and torture of its own citizens after the al-Qaida attacks of September 2001 has been spelled out in stark detail with the disclosure during high court proceedings of a mass of highly classified documents.

Previously secret papers that have been disclosed include a number implicating Tony Blair's office in many of the events that are to be the subject of the judicial inquiry that David Cameron announced last week.

Among the most damning documents are a series of interrogation reports from MI5 officers that betray their disregard for the suffering of a British resident whom they were questioning at a US airbase in Afghanistan. The documents also show that the officers were content to see the mistreatment continue.

One of the most startling documents is chapter 32 of MI6's general procedural manual, entitled "Detainees and Detention Operations", which advises officers that among the "particular sensitivities" they need to consider before becoming directly involved in an operation to detain a terrorism suspect is the question of whether "detention, rather than killing, is the objective of the operation".

Other disclosed documents show how:

• The Foreign Office decided in January 2002 that the transfer of British citizens from Afghanistan to Guantánamo was its "preferred option".

• Jack Straw asked for that rendition to be delayed until MI5 had been able to interrogate those citizens.

• Downing Street was said to have overruled FO attempts to provide a British citizen detained in Zambia with consular support in an attempt to prevent his return to the UK, with the result that he too was "rendered" to Guantánamo.

The papers have been disclosed as a result of civil proceedings brought by six former Guantánamo inmates against MI5 and MI6, the Home Office, the Foreign Office, and the Attorney General's Office, which they allege were complicit in their illegal detention and torture.

The government has been responding to disclosure requests by maintaining that it has identified up to 500,000 documents that may be relevant, and says it has deployed 60 lawyers to scrutinise them, a process that it suggests could take until the end of the decade. It has failed to hand over many of the documents that the men's lawyers have asked for, and on Friday failed to meet a deadline imposed by the high court for the disclosure of the secret interrogation policy that governed MI5 and MI6 officers between 2004 and earlier this year.

So far just 900 papers have been disclosed, and these have included batches of press cuttings and copies of government reports that were published several years ago. However, a number of highly revealing documents are among the released papers, as well as fragments of heavily censored emails, memos and policy documents.

Some are difficult to decipher, but together they paint a picture of a government that was determined not only to stand shoulder to shoulder with the United States as it embarked upon its programme of "extraordinary rendition" and torture of terrorism suspects in the immediate aftermath of 9/11, but to actively participate in that programme.

In May, after the appeal court dismissed attempts to suppress evidence of complicity in their mistreatment, the government indicated that it would attempt to settle out of court.

Today the government failed in an attempt to bring a temporary halt to the proceedings that have resulted in the disclosure of the documents. Its lawyers argued that the case should be delayed while attempts were made to mediate with the six men, in the hope that their claims could be withdrawn in advance of the judicial inquiry. Lawyers for the former Guantánamo inmates said it was far from certain that mediation would succeed, and insisted the disclosure process continue.

In rejecting the government's application, the court said it had considered the need for its lawyers to press ahead with the task of processing the 500,000 documents in any event, as the cases of the six men are among those that will be considered by the inquiry headed by Sir Peter Gibson. Last week, in announcing the inquiry, Cameron told MPs: "This inquiry will be able to look at all the information relevant to its work, including secret information. It will have access to all relevant government papers – including those held by the intelligence services."

Cameron also made clear that the sort of material that has so far been made public with the limited disclosure in the Guantánamo cases would be kept firmly under wraps during the inquiry. "Let's be frank, it is not possible to have a full public inquiry into something that is meant to be secret," he said. "So any intelligence material provided to the inquiry panel will not be made public and nor will intelligence officers be asked to give evidence in public."

The coalition government is anxious to draw a line under what is currently described in Whitehall as "detainee legacy issues". It hopes that mediation, followed by the inquiry, will lift the burden of litigation that it is currently facing while restoring public confidence in MI5 and MI6.

It also wishes to preserve what it calls "liaison relationships" – operational links with overseas intelligence agencies, including those known to use torture – on the grounds that they are a vital part of the country's counterterrorism strategy.