Miliband revealed details of the flights to the island in the Indian Ocean in a statement to parliament on Thursday.
"Contrary to earlier explicit assurances that Diego Garcia had not been used for rendition flights, recent US investigations have now revealed two occasions, both in 2002, when this had in fact occurred," he said.
"In both cases a US plane with a single detainee on board refuelled at the US facility in Diego Garcia," Miliband said.
"An error in the earlier US records search meant that these cases did not come to light"
David Miliband, British foreign secretary
Miliband said he was "very sorry indeed" to have to correct earlier government denials on the basis of new information passed to Britain by the US government on February 15.
"An error in the earlier US records search meant that these cases did not come to light," he said.
Gordon Brown, the British prime minister, said he was disappointed and that it was unfortunate that US rendition flights happened without UK knowledge.
Mark Seddon, Al Jazeera's correspondent in London, said: "The foreign minister said they are now going to trek through all records of flights just to make sure there haven't been any other errors.
"The big question remains as to the claims that have been made, which the CIA denies, that prisoners have been held at Diego Garcia. The claim is that prisoners have been held either on land or on vessels off the coast.
"There's a pretty easy way to find out. There's a British magistrate on the island. There are at least fifty police and a naval patrol. If the claims are true the government could be liable to legal action in the courts here."
British police said last year they had found no evidence to support claims that American CIA planes transporting terrorism suspects to face possible torture in secret prisons in Europe landed illegally at British airports.