Dozens of questions about the UK's involvement in the rendition and torture of terrorism suspects after 9/11 remain unanswered, an official inquiry has concluded.

In his interim report, the inquiry head, Sir Peter Gibson, raised 27 questions to be asked of the involvement of government ministers and officers from MI5 and MI6 in the mistreatment of detainees in the so-called war on terror.

After examining around 20,000 confidential documents, Gibson questioned whether the UK had "a deliberate or agreed policy" of turning a blind eye to the mistreatment of prisoners, and whether the two intelligence agencies were willing to "condone, encourage or take advantage of rendition operations" mounted by others.

The Guardian understands that the heads of the MI6 and MI5 have each been given a month to provide answers to the questions.

Whether those answers will be made public remains unclear, however: the answers are to be provided to the intelligence and security committee, the Westminster body that is supposed to provide oversight of intelligence bodies, but the ISC's reports are censored in line with recommendations from the agencies themselves.

Gibson's conclusions and the question he says now need to be address will make uncomfortable reading for former heads of the UK's intelligence agencies and for ministers of the last Labour government. It is clear that the retired appeal court judge does not accept that the blanket response that ministers gave for years to specific allegations – that Britain "does not participate in, solicit, encourage or condone the use of torture for any purpose" – is no longer sufficient.

Gibson concluded that the unanswered questions can be grouped into four broad themes: interrogation; rendition; the training of intelligence officers and the guidance they received; and communications between the intelligence agencies and government.

He also highlighted the rendition of two Libyan nationals who were taken to Tripoli against their will, along with their families, in 2004.

"There are serious allegations of UK involvement in rendition in relation to the two Libya nationals. These plainly required investigation," he said.

The report discloses that a few months after 9/11, Jack Straw, the foreign secretary, wrote to the home secretary, David Blunkett, requesting a "feasibility study" to establish whether English law could be amended to permit rendition to the UK. Blunkett wrote back saying: "The obstacles to this suggestion are simply too formidable."

Other questions that Gibson said demanded answers included "whether there was an apparent willingness, at least at some levels within the agencies, to condone, encourage or take advantage of a rendition operation" conducted by other countries. He also questioned whether the British government and its intelligence agencies became "inappropriately involved" in such renditions.

Gibson's report is based on the reading of around 20,000 documents. He was not able to take oral evidence and his inquiry was suspended in January last year after Scotland Yard opened investigations into the Libyan rendition operations.

As a consequence, his report reaches no conclusions, and no individuals are singled out for blame – instead he poses a series of questions about ministers of the last government and senior intelligence officers.

His report makes clear that the documents he has read show that British intelligence officers continued to be involved in the interrogation of detainees despite their mistreatment having been witnessed.

He also reports that the documents raise serious questions as to whether the intelligence and security committee was at times kept completely in the dark about the mistreatment of detainees and the agencies' involvement in that mistreatment.

Now that Gibson has reported it will be the ISC that will be invited to complete his investigation – a move that is being condemned by human rights groups, and has led to claims that the government is exposing itself to allegations of a cover-up.

When David Cameron announced the establishment of the inquiry, a few weeks after the coalition government was formed, he told MPs: "I do not think for a moment that we should believe that the ISC should be doing this piece of work. For public confidence, and for independence from parliament, party and government, it is right to have a judge-led inquiry."

Today, however, the ISC chairman, Sir Malcolm Rifkind, insists that such criticisms are outdated, and that his committee now had the powers, the staff and the will to conduct thorough and effective investigations.

Gibson's report is being published on the final day that parliament is sitting this year. Gibson said of it: "There are matters which deserve further investigation. That is what the documents have disclosed and we explain why in our report."

Janet Paraskeva, who was also on the inquiry panel, added: "We have worked hard to put as much as possible into the public domain. I do hope the government will decide to build on our work in a future inquiry and give the detainees a chance to have their say."

The details in their report are bound to make uncomfortable reading for Britain's intelligence agencies.

Gibson found documents that indicated some UK intelligence officers were aware of inappropriate interrogation techniques and mistreatment or allegations of mistreatment of some detainees by partners from other countries. He also found papers that suggested the government or its agencies may have become inappropriately involved in some cases of rendition.

Though Gibson said there was no reason to doubt that personnel were told detainees must be treated humanely, he said officers on the ground needed clear guidance on when and with whom to raise concerns.

A number of pages of Gibson's report were censored before publication. The Cabinet Office said the redactions had been made for national security reasons, but it was not immediately clear how substantial the cuts have been.

On Thursday in a statement to MPs, Ken Clarke, the cabinet minister without portfolio, confirmed the official inquiry into the UK's involvement in rendition and torture in the years after 9/11 would now be handed to the ISC. He said he hoped the committee's inquiry would be concluded within a year.

The Guardian understands the ISC initially refused the government's request to take on the Gibson investigation, saying that it would be overwhelmed.

The committee is already undertaking wide-ranging inquiries into mass surveillance, as well as its annual reports into the UK's intelligence community.

It is understood ministers have agreed to provide more resources and staff to allow the ISC to include Gibson in its portfolio.

The 27 questions posed by Gibson have already been sent to Britain's intelligence agencies – MI5, MI6 and GCHQ. The ISC expects to have their responses in about a month.

The two rendition operations in which the Libyan dissidents and their families were kidnapped and taken to Gaddafi's jails were mounted either side of Tony Blair's first visit Libya, in which he embraced the dictator, declared that they had found common cause in the fight against terrorism, and announced a £550m gas exploration deal for Shell.

The wife of one of the dissidents was heavily pregnant at the time of the abduction; the other dissident was kidnapped along with his wife and four children, the youngest a girl aged six. Both men were leading members of an Islamist group, the Libyan Islamic Fighting Group.

Among the secret papers about their abduction that were discovered during the Libyan revolution was a signed letter from the then head of counter-terrorism at MI6, Mark Allen, in which he boasted of his agency's role in one of the operations.

There were also secret CIA faxes describing the second operation as a joint UK-Libyan venture. One man received a £2.2m payment after suing the British government; government lawyers are trying to keep the claim by the second victim from being heard in the English courts.

The discovery and publication of the Tripoli documents came as a profound shock to MI6. However, there have been allegations of MI6 and MI5 involvement in a series of other operations in Pakistan, Egypt, Morocco and Bangladesh, as well as Guantánamo Bay and Afghanistan, which have resulted in terrorism suspects suffering severe mistreatment.

In some cases – the most notorious being that of the British resident Binyam Mohamed – the allegations have been found to be true, while in others the government has paid sums totalling several million pounds in order to settle compensation claims out of court.