A British government guidance paper that is intended to prevent the country’s intelligence officers from becoming involved in human rights abuses is being rewritten in secret, much to the alarm of civil liberties groups.

Rights activists are deeply worried that the UK government may be tempted to water down the guidance at a time when the US president, Donald Trump, has said he hopes to restore waterboarding – “and a hell of a lot worse” – and has nominated Gina Haspel as the next head of the CIA. Haspel reportedly oversaw a secret CIA prison in Thailand, where a terrorism suspect was tortured.

The UK paper, known in Whitehall as the ”consolidated guidance”, was rewritten and made public by the coalition government following a series of scandals in the years following the 9/11 attack on the twin towers in New York.

Under the terms of the previous version, drawn up early in 2002, MI6 officers had helped to plan a number of so-called rendition operations. Officers from MI5 and MI6 had also become embroiled in the torture of detainees held overseas, usually by handing questions to overseas intelligence agencies with poor human rights records.

On publishing the current version of the consolidated guidance, David Cameron, then prime minister, told MPs: “We are determined to resolve the problems of the past so are we determined to have greater clarity about what is and what is not acceptable in the future.”

Cameron said that in future, MI5 and MI6 officers should not do anything that they believe could lead to an individual being tortured, and that only ministers could decide what steps to take if the agencies wanted to interrogate prisoners who could hold information crucial to saving lives.

The consolidated guidance is now being redrafted again after a 2016 report by the intelligence services commissioner, Sir Mark Waller, was critical of both the wording of the guidance and MI6’s dealings with a Kenyan anti-terrorism unit.

The Camp Delta US military-run prison at Guantánamo Bay, Cuba, in 2006. Photograph: Brennan Linsley/AP

So far, however, government departments, the intelligence agencies and Scotland Yard’s counter-terrorism command are the only bodies known to have been consulted.

Waller had also recommended that “in order to improve transparency and accountability”, the Cabinet Office should consult rights groups about the new version, and suggested the Equality and Human Rights Commission, Fair Trials Abroad, Prisoners Abroad, Redress and Reprieve.

However, none of these organisations have been consulted and a number of groups are concerned that the guidance may be weakened during the process.

In a joint letter to Boris Johnson, the foreign secretary, five human rights groups – including Fair Trials Abroad, Reprieve and Redress, as well as Amnesty International and Liberty – have warned: “The deep and lasting stain of UK complicity in extraordinary rendition and torture over the so-called war on terror powerfully demonstrates the need for safeguards.

“We therefore have serious concerns that the government may be seeking to amend or even water down its guidance on torture behind closed doors.

“The government has provided no justification for why it has failed to adhere to the recommendations of its own commissioner and engage in a meaningful and transparent consultation, and chosen instead to talk only to itself and its own intelligence agencies.”

At the legal charity Reprieve, director Maya Foa said: “Donald Trump has nominated one of George Bush’s torturers-in-chief to lead the CIA. Gina Haspel oversaw a ‘black site’ in Thailand and helped destroy video evidence of detainees being subjected to beatings and extreme abuse. As the US regresses, the UK government must stand firm and reject torture in all its forms.

“The government’s secret internal review risks watering down the high standards expected of the UK’s intelligence agencies,” she added. “It must be opened up to full public consultation without delay.”

The Cabinet Office declined to say why rights groups were not being consulted in line with Waller’s recommendation. A government spokeswoman said: “Work is ongoing to identify what, if any, further changes could be made to the consolidated guidance, following the intelligence services commissioner’s recommendations.

“We have engaged with both the intelligence services commissioner and the office of the investigatory powers commissioner, to whom the prime minister has issued a direction to continue the statutory oversight of the consolidated guidance.”

She added that the government would consider any comments from parliament’s intelligence and security committee, the group of MPs and peers that provides oversight of the intelligence agencies, and that the guidance paper would be made public once it had been rewritten.

The existence of official guidance for intelligence officers seeking information from detainees held by overseas intelligence agencies became known publicly in 2009, during the cross-examination of an MI5 officer who had interrogated a British resident, Binyam Mohamed, who was being tortured by CIA officers at a prison in Pakistan.

The coalition government acted to rewrite the consolidated guidance and make it public in 2010 after the Guardian highlighted a series of cases in which terrorism suspects were tortured by overseas intelligence agencies while being asked questions that had been drawn up by the UK’s intelligence agencies. The victims included one man, later convicted and jailed for life for terrorism offences, who had three fingernails pulled out by Pakistani intelligence officers after MI5 had drawn up a series of questions to be put to him, and MI6 had handed the questions over to the Pakistani authorities.

The following year the Guardian obtained a copy of the post-9/11 guidance, which showed that senior intelligence officers were expected to weigh the importance of the information being sought against the level of mistreatment the detainee was likely to suffer while it was being extracted.

The document also warned that the agencies’ reputation was likely to be damaged if the existence of the guidance was disclosed.

Later that year, a number of MI6 and CIA documents discovered during the Libyan revolution exposed the way in which MI6 had assisted in the kidnap of two of Muammar Gaddafi’s Islamist opponents, who were flown to a Tripoli prison, along with their wives – one of whom was pregnant – and four children.