The country's leading civil and human rights organisations have written to the judge who is to head an investigation into the UK's involvement in torture and rendition, setting out what they believe his inquiry must achieve to be effective.

Nine NGOs, including Amnesty International, Liberty, Justice and Reprieve, have told Sir Peter Gibson that his efforts need not only be independent, thorough and subject to public scrutiny, but should also allow for the participation of victims.

"Survivors or victims must be involved in the process to ensure their right to effective investigation and redress, and special measures must be adopted to ensure this participation is supportive, safe and effective," the NGOs wrote.

They also said that the inquiry must be able to blame the British state, where appropriate, as well as senior officials who bear responsibility for any crimes committed, and hold them to account.

"It must be able to pronounce on state responsibility for knowledge and involvement in the serious human rights violations that have been alleged and to identify any individuals responsible for such abuses, including establishing the responsibility of superior officers for crimes committed by subordinates under their effective control," they wrote.

Among the inquiry's purposes must be "the need to hold accountable those responsible for serious human rights violations".

The NGOs added that they believe the inquiry should:

• Hear as much evidence as possible in public.

• Aim to achieve maximum public disclosure.

• Not allow its independence or thoroughness to be compromised by government or intelligence agency attempts to invoke secrecy.

• Decide for itself which documents it will publish.

• Ask agents of foreign intelligence agencies to give evidence.

• Compel the co-operation of corporations doing business in the UK who are alleged to have been involved in the abuses.

The NGOs also said they believe that both victims of torture and the intelligence agencies should have the right to legal representation funded by the inquiry.

They also said that it is "imperative" that the inquiry's report be published and that any redactions for national security reasons should be agreed by Gibson and his two inquiry colleagues, and must also be "subject to review by a court".

The letter added: "A sufficiently empowered and transparent inquiry could discharge the UK's duty to effectively investigate damaging allegations of knowledge and/or involvement by state actors or agents in the torture, ill-treatment or rendition of individuals that have arisen in the last decade. Such an inquiry could also play an important role in clarifying how involvement in torture, ill-treatment or rendition might be prevented in the future."

One of the NGOs, the legal charity Reprieve, had objected to the appointment of Gibson to head the inquiry, saying he was "fatally compromised" as he also serves as intelligence services commissioner, reviewing the issue of surveillance warrants to the intelligence agencies. Government lawyers dismissed the criticism as "unwarranted and baseless".

Although David Cameron has said he hopes the inquiry will be under way before the end of the year, and that he hopes Gibson will report back within 12 months, its start is likely to be delayed by litigation.

Six British citizens and residents who were "rendered" to Guantánamo are suing the UK government over its role in their mistreatment. Their lawyers say their litigation cannot be replaced by mediation until the government hands over more of the thousands of documents about their cases that it acknowledges it holds.

In addition, a number of other alleged torture victims are considering suing the government, and Scotland Yard is still investigating an MI5 officer and an MI6 officer over allegations of possible criminal wrongdoing.