United Nations human rights investigators have concluded that the British government has been complicit in the mistreatment and possible torture of several of its own citizens during the "war on terror".

In a report published today that will make difficult reading for ministers who repeatedly denied the UK's involvement in torture, UN officials have indicated that there is clear evidence of the UK's role in the secret detention overseas of several British Muslims.

The officials say that such secret imprisonment – or "proxy detentions" – not only facilitates torture, but may amount to torture in its own right. In one starkly worded passage, they warn that if a state's use of proxy detention had been systematic or widespread it would amount to a "crime against humanity".

The 226-page UN report follows the publication two months ago of a dossier entitled Cruel Britannia, from the New York-based NGO Human Rights Watch, whose researchers interviewed several Pakistani intelligence agents who alleged that they had tortured British terrorism suspects on behalf of their UK counterparts. It also follows a series of disclosures in the Guardian about the role played by officers of MI5, MI6 and Greater Manchester police in the detention and questioning under torture of terrorism suspects held in Pakistan and elsewhere.

The UN investigation into torture and rendition across the globe since 9/11 lasted several years and was led by Martin Scheinin, UN special rapporteur on terrorism and human rights, and Manfred Nowak, special rapporteur on torture. In a move that will do little to ease the discomfort of western governments that were the focus of the investigation, the two men and their aides were assisted by members of a UN working party on secret detentions that was first set up in 1979 to investigate the fate of people who were "disappeared" by the Pinochet regime in Chile.

Their report concludes that secret detention "amounts to a case of enforced disappearance" and that it is "a manifold human rights violation that cannot be justified under any circumstances, including during states of emergency".

Listing those cases in which they conclude that a state has been complicit in a secret detention, the authors highlight "the United Kingdom in the cases of several individuals, including Binyam Mohamed, Salahuddin Amin, Zeeshan Siddiqui, Rangzieb Ahmed and Rashid Rauf".

Ahmed, 34, from Rochdale, Greater Manchester, was detained in Pakistan in 2006. MPs have heard that after evidence of his terrorist offences had been gathered he was allowed to fly from Manchester to Islamabad, and that MI6 then suggested to a notorious Pakistani intelligence agency that its officers should detain him as he was a dangerous terrorist.

After MI5 and Greater Manchester police drew up a list of questions to be put to Ahmed, the Pakistani agents who were questioning him ripped out a number of his fingernails. Ahmed alleges he was also beaten, whipped and deprived of sleep. He was later deported to the UK, tried and convicted of terrorism offences and is now serving a life sentence at Full Sutton prison near York.

Salahuddin Amin, 35, from Luton, Bedfordshire, was deported to the UK in February 2005 after spending 10 months in the custody of Pakistan's Inter-Services Intelligence Directorate (ISI). The UK courts have heard that he was questioned 11 times by MI5 officers, and Amin says he was tortured before each session. Human Rights Watch says it has spoken to Pakistani intelligence officers who broadly corroborate his account. Amin was also tried and convicted and is serving a life sentence at Whitemoor prison in Cambridgeshire.

The British government is attempting to block the disclosure of classified US documents about Binyam Mohamed, leading to speculation that they contain evidence that senior figures in Tony Blair's administration had some knowledge of Mohamed's torture in Pakistan in 2002.

The whereabouts of Rauf and Siddiqui are unknown.

Scotland Yard detectives are investigating MI5's role in the mistreatment of Mohamed and one other unnamed individual.

The UN report contains warnings that inquiries into these two cases may not be sufficient to meet the UK's obligations under international law, however, saying that the British government and other states would face claims of responsibility "when the state received claims that someone had been subjected to torture or other ill-treatment, or an enforced disappearance, or otherwise received information suggesting that such acts may have taken place but failed to have the claims impartially investigated".

The UN report adds: "According to the European court, authorities must always make a serious attempt to find out what happened and should not rely on hasty or ill-founded conclusions to close their investigation or as the basis of their decisions."

The report details the role of many other governments in the kidnapping and secret detention of terrorism suspects. Among those highlighted alongside the UK are the US, Algeria, China, Iran, Sudan and Zimbabwe.

The Foreign Office described the report as "unsubstantiated and irresponsible" and maintained that the authors had not substantiated their claims during meetings with FO officials. "As far as allegations against the UK are concerned, the report contains no new information and repeats unproven allegations as if they were fact. The UK's position on secret detention is clear: we oppose any deprivation of liberty that amounts to placing individuals beyond the protection of the law."

Despite the FO's assertion that there is no evidence to support the UN's allegations, the attorney general has asked Scotland Yard detectives to investigate a number of cases.

A spokeswoman for Reprieve, the legal charity that represents Binyam Mohamed, said: "The findings make uncomfortable reading for states like the UK who – despite their public condemnation of such practices – are revealed as complicit in war crimes like kidnap, secret detention, and torture.

"Worryingly, the report indicates that the UK intelligence services lack the oversight that would prevent crimes like complicity in torture from recurring in the future."