The Foreign Office was accused of a cover-up after ministers said records of flights passing through an overseas territory used by the United States 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 US has a vast military base on Diego Garcia which is part of the British Indian Ocean Territory.
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 on extraordinary rendition, who requested a list of flights which passed through Diego Garcia from January 2002 to January 2009.
Mr Simmonds told him in a written answer: "Records on flight departures and arrivals on Diego Garcia are held by the British Indian Ocean Territory immigration authorities.
"Daily occurrence logs, which record the flights landing and taking off, cover the period since 2003. Though there are some limited records from 2002, I understand they are incomplete due to water damage."
Cori Crider, a director at legal charity Reprieve, which is representing Libyan dissident Abdel Hakim Belhadj who claims he was on a rendition flight through Diego Garcia, said : "It's looking worse and worse for the UK government on Diego Garcia.
"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."
A Foreign Office spokeswoman said: "The British Indian Ocean Territory administration is responsible for records of flights on Diego Garcia and they are investigating the full extent of the damage, how many records and what information is affected.
"The damage was only recently discovered so it is unknown how exactly or when it occurred.
"With or without flight records we have firm assurances from the US government, as recently as December 2013, that apart from two instances of rendition through Diego Garcia in 2002 there have been no other instances in which US intelligence flights landed in the UK, our overseas territories or crown dependencies with a detainee on board since September 11, 2001."
Last month MPs said the US must provide binding commitments over its future use of Diego Garcia if it is to be allowed to carry on using its military base on the island.
The Commons Foreign Affairs Committee said public confidence had been "dented" by the disclosure in 2008 that the US had secretly used the island as part of its rendition programme without informing British ministers - in contravention of previous assurances.
The committee said the Government should use the forthcoming negotiations on the renewal of the 50-year agreement allowing the US to use the island - which runs to 2016 - to tighten up the previous informal arrangements.
It said a requirement to obtain the prior approval of the UK Government for the use of the island in combat operations or other "politically sensitive activity" should be written into the new agreement - with an explicit condition that it must not be used for rendition without authorisation from UK ministers.
In 2006, the then foreign secretary Jack Straw told MPs that there was no evidence the US had used any British overseas territory in the rendition of terrorist suspects following the 9/11 attacks in 2001.
Two years later, however, the then incumbent David Miliband disclosed that the US had since admitted it had used Diego Garcia for the re-fuelling of rendition flights on two occasions in 2002 without informing the UK.
Mr Tyrie said: " It has been seven years since I first started asking questions about Diego Garcia in Parliament. In 2007, the Government assured Parliament that Diego Garcia had not been used in the rendition programme.
"The following year they were forced to make a statement flatly contradicting this and admit that two US rendition flights landed on the island in 2002, despite assurances to the contrary.
"When I asked the Foreign Office for Diego Garcia flight records in 2008, I was told that a thorough review had been conducted which had found no such information.
"This time there is better news. It turns out that records have been kept. But the silver lining has a large cloud. Today, we have learned that we may never get the full truth because flight records from 2002 are 'incomplete due to water damage'.
"The Security Service has previously been criticised for its poor record keeping, which impeded an effective investigation into allegations of British complicity in rendition. It seems that poor record keeping is once again making it difficult to get to the truth about the UK's country's involvement in the rendition programme.
"Recent reports that the CIA maintained a so-called black site on Diego Garcia with the full cooperation of the British Government are deeply disturbing. We need to know if this is true.
"One way or another, the truth will eventually come out. The security services don't want to be involved in these practices. The services want the public to have confidence in them. Accountability is to their benefit.
"That is why an investigation into extraordinary rendition is not only morally right but expedient on grounds of national security."
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