Prime Minister Gordon Brown said he was disappointed by the US error.
"It is obviously a very serious issue," Brown told a news conference on a visit to the EU headquarters in Brussels.
"The United States has expressed regret about us not knowing about these issues. We share the disappointment that everybody has about what actually happened.
"I think the important thing is now that we put in place the best possible procedures to ensure that this could not happen again," he said.
The White House acknowledged its fault, but stressed there would be no impact of counter-terrorism cooperation with Britain.
"It's unfortunate mistakes were made in the reporting of the information," said national security spokesman Gordon Johndroe, who referred follow-up questions to the CIA.
One of the prisoners involved in the rendition flights is still being held at the US-run detention camp at Guantanamo Bay on Cuba while the other has since been released.
Extraordinary rendition, whereby suspects are transferred covertly to a third country or to US-run detention centres, has been controversial since it began in the aftermath of the September 11, 2001 attacks in the United States.
Human rights groups say it allows prisoners to be transferred outside the rule of law and exposes them to the risk of torture.
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"George Bush has declared the war on terrorism to be the cause of his generation. The cause of Canadian sovereignty will be ours." - John Godfrey, MP for Don Va