A British territory in the Indian Ocean was used for American "torture" flights, despite categorical denials of Britain's involvement from both Tony Blair and Jack Straw, the Government admitted yesterday.

The Foreign Secretary, David Miliband, had to make a humiliating apology to the Commons after it emerged that the US failed to tell British officials that two CIA rendition flights carrying suspected terrorists landed on the island of Diego Garcia in 2002. Six years on, one of the suspects is still being held by the US at Guantanamo Bay in Cuba. The other has been released.

Mr Miliband denied there was a deliberate cover-up and said he believed the US had acted "in good faith". However, Gordon Brown, attending an EU summit in Brussels, expressed his "disappointment" and said Washington's failure to disclose the flights earlier was "a very serious issue".

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"The US has expressed regret that it did not admit at the time to these renditions through Diego Garcia," he added. "We have to assure ourselves these procedures will never happen again."

America has used rendition flights to interrogate terror suspects – in particular since the attacks of 11 September 2001. The two flights which have now come to light, following an audit by officials in Washington, stopped to refuel on Diego Garcia on their way to Guantanamo Bay.

Mr Miliband said he was "very sorry indeed" to have to correct previous statements made by the then Prime Minister Mr Blair and Foreign Secretary Jack Straw that rendition flights had not used British bases. He said the Diego Garcia cases had not come to light earlier because of an error in a previous US records search. "The House and the Government will share deep disappointment at this news and about its late emergence," he added. "That disappointment is shared by our US allies. They recognise the absolute imperative for the Government to provide accurate information to Parliament."

Mr Miliband said each case involved a single detainee – neither of them British – who did not leave the aircraft while it was on the ground. He told MPs that neither suspect was subject to torture by "water-boarding". Nevertheless, he said he had told officials to draw up a list of all flights about which concerns had been expressed regarding the use of UK territory.

In future, he added, Britain would approve CIA rendition flights through British bases only if the Government was satisfied they complied with British laws and the UK's international obligations, including those under the UN Convention Against Torture.

Human rights activists voiced concern that the two cases which had been identified might only be the "tip of the iceberg". Kate Allen, of Amnesty International UK, said: "It is not enough for the Government simply to accept US assurances on correct behaviour in the war on terror. We should retain our own integrity and act accordingly."

As recently as January 2007, Mr Blair assured the Intelligence and Security Committee he was satisfied that the US had at no time since 9/11 rendered an individual though the UK or its overseas territories.