The British government's problems with missing files deepened dramatically when the Foreign Office claimed documents on the UK's role in the CIA's global abduction operation had been destroyed accidentally when they became soaked with water.

In a statement that human rights groups said "smacked of a cover-up", the department maintained that records of post-9/11 flights in and out of Diego Garcia, the British territory in the Indian Ocean, were "incomplete due to water damage".

The claim comes amid media reports in the US that a Senate report due to be published later this year identifies Diego Garcia as a location where the CIA established a secret prison as part of its extraordinary rendition programme. According to one report, classified CIA documents state that the prison was established with the "full cooperation" of the UK government.

It also comes at a time when MPs are demanding the Home Office urgently provide more information about 114 "missing" files that could have contained information about an alleged child abuse network in the 1980s.

Ministers of successive governments have repeatedly given misleading or incomplete information about the CIA's use of Diego Garcia. In February 2008, the then foreign secretary, David Miliband, was forced to apologise to MPs and explain that Tony Blair's "earlier explicit assurances that Diego Garcia had not been used for rendition flights" had not been correct. Miliband said at this point that two rendition flights had landed, but that the detainees on board had not disembarked.

Miliband's admission was made after human rights groups produced irrefutable evidence that aircraft linked to the rendition programme had landed on Diego Garcia. Since then, far more aircraft have been shown to have been involved in the operation.

The "water damage" claim was given in response to a parliamentary question by the Tory chair of the Treasury select committee, Andrew Tyrie, who has been investigating the UK's involvement in the rendition programme for several years.

When Tyrie asked the Foreign Office (FCO) to explain which government department keeps a list of flights which passed through Diego Garcia from January 2002 to January 2009, FCO minister Mark Simmonds replied: "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."

The Foreign Office would not say whether the damaged files were UK or US records, or say where they were located. An FO spokesperson maintained that because the damage "was only recently discovered" it did not know how or when it occurred.

Cori Crider of the legal charity Reprieve 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."

Crider added that the claim that documents had been destroyed accidentally was "especially disturbing" given that Scotland Yard is investigating the role played by MI6 in the abduction of a Libyan dissident, Abdel Hakim Belhaj, who was flown to one of Muammar Gaddafi's prisons along with his pregnant wife in 2004.

The police investigation, Operation Lydd, is thought to have examined whether the couple were flown via Diego Garcia. A report is due to be handed shortly to the director of public prosecutions.

The White House and the CIA are working on final redactions to a 481-page executive summary of a classified report by the US Senate committee on intelligence on the rendition programme prior to its publication, possibly in September. The full 6,300-page report is said to be scathing of the way in which the CIA resorted rapidly to the abduction and torture of al-Qaida suspects after the attacks of 2001.

There have been a number of reports suggesting that allies of the US, including the UK and Poland, and been lobbying to ensure that all reference to their own involvement is removed from the summary before it is published. The Foreign Office claimed that it had merely been seeking assurances that "ordinary clearance procedures will be followed" if the report contains material supplied by the UK.

The British government is particularly sensitive about the allegations that Diego Garcia hosted one of the CIA's prisons, at times claiming that it knows only that which it is told by Washington. Although the island has operated as a US military base since the islanders were evicted in the 1960s, it remains a British territory, and its use during the rendition programme would have placed the UK in breach of a raft of international and domestic laws.

Belhaj and his wife are suing MI6, the agency's former head of counter-terrorism Sir Mark Allen and Jack Straw, who was foreign secretary at the time that the couple were abducted.

Last month, the Commons cross-party defence committee suggested that information about the extent to which the CIA used the island as a "black site" to transfer detainees was still being withheld. "Recent developments have once again brought into question the validity of assurances by the US about its use of Diego Garcia," it said.

The committee warned that it will assess the implications for Britain and for "public confidence" in its previous statements on US use of Diego Garcia, and said the US should not in future be permitted to use the island, to transfer terror suspects, for combat operations, "or any other politically sensitive activity", without the explicit authorisation from the UK government.

Although Miliband told MPs that detainees had not been held on Diego Garcia, others have contradicted this assertion.

Manfred Nowak, as United Nations special rapporteur on torture, said he had received "credible evidence from well-placed sources familiar with the situation on the island" that CIA detainees had been held there between 2002 and 2003.

General Barry McCaffrey, a former head of Southcom, the US military's southern command, has twice stated publicly that Diego Garcia has been used by the US to hold prisoners, saying in one radio interview in May 2004: "We're probably holding around 3,000 people, you know, Bagram air field, Diego Garcia, Guantánamo, 16 camps throughout Iraq."

In 2003, Time magazine quoted "a regional intelligence official" as saying that a man accused of plotting the 2002 Bali nightclub bombing was being interrogated on Diego Garcia. Five years later the magazine reported that a CIA counter-terrorism official said a high-value prisoner or prisoners were being held and interrogated on the island.

In August 2008, the Observer reported that former US intelligence officers "unofficially told senior Spanish judge Baltasar Garzón that Mustafa Setmarian, a Spanish-based Syrian accused of running terrorist training camps in Afghanistan, was taken to Diego Garcia in late 2005 and held there for months".

As a consequence of the repeated allegations, the foreign affairs select committee said in 2009 that it was "unacceptable" that the government had not taken steps to obtain the full details of the two individuals whom it had admitted to have been rendered through Diego Garcia.

The committee added: "We conclude that the use of Diego Garcia for US rendition flights without the knowledge or consent of the British government raises disquieting questions about the effectiveness of the government's exercise of its responsibilities in relation to this territory."