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Inquiries to centre on mistreatment of prisoners at US-run detention centre in Bagram, north of Kabul, in 2002
Scotland Yard has opened investigations into three further allegations that British intelligence officers were involved in the mistreatment of al-Qaida suspects after 9/11, bringing to four the number of police inquiries currently faced by MI5 and MI6.
The three additional investigations focus on events during the early weeks of 2002 at a US-run detention centre at Bagram, north of Kabul, where prisoners were interrogated and allegedly tortured.
A 10-strong detective team is already investigating two so-called rendition operations in 2004, in which MI6 worked with Muammar Gaddafi's intelligence agents to arrange for two Libyan dissidents and their families to be kidnapped and flown to Tripoli.
One of the latest three investigations is thought to concern a British Muslim who is alleged to have been subjected to mistreatment at Bagram, and who is said to have subsequently agreed to work as an informant for MI5 in order to avoid further suffering.
The second concerns Shaker Aamer, a Saudi national and UK resident who was detained and allegedly mistreated at Bagram, before being flown to Guantánamo. He remains at Guantánamo, with his lawyers alleging that a deal struck between the US, UK and Saudi authorities is preventing his return to his family in London.
Aamer, 44, alleges that British intelligence officers were present while he was abused at Bagram. Scotland Yard detectives are also thought to be considering his treatment at Guantánamo, where he was interrogated by British intelligence officers. Yard officers are known to have travelled to Guantánamo at least once and taken a statement from Aamer.
The third investigation is examining allegations made by Hassan Zemiri, 45, an Algerian married to a Canadian who was detained at Bagram and Guantánamo before being released. Zemiri alleges that British intelligence officers interrogated him while he was being beaten and, on one occasion, water-boarded, at Bagram. He also alleges that an Englishman calling himself Paul took part in the beatings.
A joint panel of police and Crown prosecutors has examined at least 12 allegations in addition to the Libyan rendition cases, and possibly more, but declined to mount formal investigations in at least nine cases, much to the anger of the complainants.
Such is the sensitivity surrounding the unprecedented series of investigations into the activities of the government's intelligence agencies that the Yard is refusing to disclose more than the most basic details.
A spokeswoman said: "The panel has now had the opportunity to sit and, having assessed 12 cases, it has referred three to the Metropolitan Police Service to consider further investigation. The MPS has decided to undertake further investigation into these three cases. We are not prepared to discuss individual cases."
The Yard is also refusing to make public its reasons for declining to investigate some alleged crimes. The Guardian understands, however, that those reasons include costs, the difficulty of obtaining visas to travel to take statements from some complainants and witnesses, and the lack of co-operation from some overseas intelligence agencies, including the CIA.
Two previous investigations by the Yard into allegations that British intelligence officers committed serious crimes during counter-terrorism operations following 9/11 ended without charges being brought.
The first, known as Operation Hinton, examined MI5's role in the mistreatment of British resident Binyam Mohamed in Pakistan and Morocco. It ended with the director of public prosecutions Keir Starmer announcing that there was insufficient evidence to show that an MI5 officer knew Mohamed was being tortured when he travelled to Karachi to interrogate him, or that the agency knew Mohamed was being tortured when questions were supplied to his American captors.
The second, Operation Iden, inquired into allegations that an MI6 officer was involved in the mistreatment of a Saudi suspect held at Bagram in January 2002. Although there is understood to have been documentary evidence supporting this allegation, the investigation is thought to have foundered when police were refused entry into Saudi Arabia to take a statement from the alleged victim.
The US military opened a detention centre at the former Soviet airbase at Bagram within weeks of the invasion that toppled the Taliban regime in the aftermath of 9/11.
Officers from both intelligence agencies interrogated suspects at Bagram, after Jack Straw, then foreign secretary, ordered that the removal of British prisoners to Guantánamo should be delayed long enough for questioning by a "specialist team" to take place.
The severe mistreatment of detainees at Bagram has been documented by several human rights groups and was the subject of at least one warning or complaint to London by an MI6 officer. The US army has itself acknowledged that two inmates were tortured to death.
Since March 2009, when Scotland Yard embarked on its first investigations into allegations against MI5 and MI6, detectives have spent much of their time examining events at Bagram during the early weeks of 2002, and have been attempting to gather evidence that would show exactly how British intelligence officers conducted themselves while at the prison.
The cases that the Yard, in consultation with the Crown Prosecution Service, have decided against investigating include a number concerning former detainees who were not held at Bagram. These include Martin Mubanga, a British Muslim who spent almost three years in Guantanamo.
Documents subsequently disclosed in court during proceedings brought on behalf of Mubanga and other former Guantanamo inmates showed that after he was initially detained in Zambia in March 2002, Downing Street had insisted he be denied consular assistance. Any such assistance would have impeded his unlawful removal to Guantanamo.
Mubanga's lawyer Louise Christian is angry that the Yard refused to investigate on the grounds that his case may be examined by an inquiry at some point in the future. "It is unprecedented for the police and the CPS, which are independent, to refuse to investigate a serious offence on the grounds that a private inquiry, which does not comply with standards of international law, will do so in the far distant future," she said.
The Yard has also declined to investigate the UK's role in the rendition of two alleged insurgents captured in Iraq during an SAS raid in February 2004. The two men were handed over to US forces and later flown to Bagram, in breach of the Geneva Conventions. The Ministry of Defence has admitted that it was aware that the rendition was to take place.