The Secret Intelligence Service (SIS) has referred an unidentified case involving alleged complicity in torture to the Attorney General who has in turn referred it on to the Metropolitan Police, the Daily Telegraph can disclose.
The police are already investigating MI5, the Security Service, over allegations that they colluded in the torture of the former Guantanamo detainee, Binyam Mohamed.
It is the first time that the foreign intelligence service and domestic security service have been the subject of police investigations.
The police said the MI6 case was unrelated to Mohamed and involved the conditions under which a foreign national was detained, although it did not say when or in which country.
It also did not say whether MI6 officers are alleged to have been involved in the mistreatment or simply to have facilitated the mistreatment by others.
A Metropolitan Police spokesman said: "We can confirm that the Attorney General asked the Metropolitan Police to investigate a case that was a referral from the Secret Intelligence Service.
"This is unrelated to Binyam Mohamed but looks at the conditions under which a non-British citizen was detained and the potential involvement of British personnel.
"An investigation is ongoing."
David Miliband, the Foreign Secretary, has written to William Hague, his opposite number in the Tory party, telling him the case had been referred by the Attorney General to the police.
He told Mr Hague: "This case was referred to the Attorney General by SIS on its own initiative, unprompted by any accusation against the service or the individual concerned. It is for the police to investigate.
"The Government cannot comment further both to avoid prejudice and to protect the individuals involved. The scope and handling of any police investigation is a matter for the police themselves.
He added: "The Government wholeheartedly condemns torture. We will not condone it. Neither will we ever ask others to do it on our behalf. This is not mere rhetoric but a principled stance consistent with our unequivocal commitment to human rights. We are fortunate to have the best security and intelligence services and armed forces in the world. We are all safer because of the work they do with integrity and bravery."
The existence of MI5 and MI6, which celebrate their centenary this year, was not even acknowledged until 1992 but since then the government has laid out an explicit legal framework that governs their activity.
Sir John Scarlett, the head of MI6, known as "C", said in his first interview last month that they would allow "no torture and there is no complicity with torture" in the service.
Sir John said his officers were "as committed to the values and the human rights values of liberal democracy as anybody else."
But he added: "They also have the responsibility of protecting the country against terrorism and these issues need to be debated and understood in that context."
A number of detainees have made allegations of torture, among them the al-Qaeda terrorists Rangzieb Ahmed and Salahuddin Ahmed, although British complicity in each case was rejected by the courts.
Twelve others who were detained in Guantanamo Bay are pursing damages cases through the courts including Binyam Mohamed.
Mohamed, 30, an Ethiopian refugee, claims MI5 knew he was being tortured in Morocco and fed questions to his interrogators through the CIA.
A ruling by the High Court last year said the role of MI5 went "far beyond that of a bystander or witness to the alleged wrongdoing."