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The Foreign Office said it was only recently discovered that records of flights passing through an overseas territory used by the US for extraordinary rendition had been lost to "water damage".
A spokeswoman said:
Legal charity Reprieve has claimed it is "looking worse and worse for the UK Government on Diego Garcia", after the Foreign Office was accused of a cover-up over records that were lost due to "water damage".
Reprieve represents Libyan dissident Abdel Hakim Belhadj, who claims he was on a rendition flight through Diego Garcia.
Director Cori Crider said: "First we learn the Senate's upcoming torture report says detainees were held on the island, and now - conveniently - a pile of key documents turn up missing with 'water damage'?
"The Government might as well have said the dog ate their homework. This smacks of a cover-up. They now need to come clean about how, when, and where this evidence was lost."
The Foreign Office has been accused of a cover-up after records of flights passing through an overseas territory used by the US for extraordinary rendition had been lost to "water damage".
The US has admitted using Diego Garcia for flights as part of its extraordinary rendition programme for terror suspects on two occasions in 2002.
Foreign Office Minister Mark Simmonds told MPs that only "limited records" for 2002 were available, due to the damage the files had suffered.
The disclosure that records had been lost came in response to a question from Tory MP Andrew Tyrie, the chairman of the all-party parliamentary group who requested a list of flights which passed through Diego Garcia from January 2002 to January 2009.