Fourteen governments in Europe turned a blind eye to at least 1,245 CIA flights through their airspace, some of which were used to illegally abduct terrorist suspects for questioning, according to a damning report passed by the European Parliament today.

Germany, Britain, Ireland and Portugal permitted the highest numbers of covert flights discovered during a lengthy investigation by MEPs.

The flights included the so-called “extraordinary rendition” of one British citizen and three British residents, the report claimed. It added that two of them were tortured and two are still being held at the US detention facility Guantanamo Bay, having never been formally charged with an offence.

The report also expressed "outrage" at a legal opinion given by Michael Wood, a former legal advisor to the Foreign Office. He said that "receiving or possessing" information extracted under torture was not in itself against international conventions banning torture, "in so far as there is no direct participation in the torture".

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Mr Wood refused to give evidence to the European Parliament committee which conducted the inquiry.

The document was not passed without a fight, however. It was approved by a majority of 382 against 256 with 74 abstentions amid claims on one hand that it was anti-American and full of hypothetical assumptions, and on the other that some MEPs had been encouraged by their governments to water it down.

Members of the centre right group of MEPs, the European’s People’s Party, which includes the Conservative Party, split over the vote.

Charles Tannock, a Conservative MEP for London, said: “What we have done is nothing new and cost European taxpayers over one million euros. It is all about grand-standing and undermining states in their fight against terrorism. In my view it is very long on accusations and very low on proof.”

But Baroness Sarah Ludford, a Liberal Democrat MEP for London and one of those on the committee that prepared the report, said: "The European Parliament should not be the only keepers of Europe's conscience - national MPs such as those at Westminster must take up the baton.

"The fact remains that it was on Geoff Hoon's watch as Defence Secretary that CIA planes linked to torture flights transited the UK and UK officials facilitated or failed to stop torture of British citizens and residents."

The report revealed that all EU countries had been fully informed of the practice of extraordinary rendition by Condoleezza Rice, the US Secretary of State, at a Nato-EU meeting in February 2005 and subsequently at high-level meetings in Brussels on February 8 and May 3 last year, but many chose to collaborate with the US.

It also highlighted a lack of help with the inquiry from the British Government, stating that it "deplores" the way it failed to cooperate. The report's main author Giovanni Fava, an Italian socialist MEP, also denounced “the very great reticence from almost all the member states (with the exception of Germany and Spain) to cooperate,” with the investigation.

While acknowledging that terrorism is a big threat to Europe, the report said that it must be tackled lawfully in co-operation with the United States.

It added: "After 11 September 2001, the so-called 'war on terror' - in its excesses - has produced a serious and dangerous erosion of human rights and fundamental freedoms."

As well as at least 1,245 flights operated by the CIA between the end of 2001 and the end of 2005 in European airspace, there were "an unspecified number" of military flights for the same purpose.

The report "regrets that European countries have been relinquishing their control over their airspace and airports by turning a blind eye or admitting flights operated by the CIA which, on some occasions, were being used for extraordinary rendition or the illegal transportation of detainees".

It expressed "serious concern" about 170 stopovers made by CIA-operated aircraft at UK airports, "which on many occasions came from or were bound for countries linked with extraordinary rendition circuits and the transfer of detainees".

It also expressed "serious concern" about 147 stopovers at Irish airports.

Ahead of the vote, Franco Frattini, the EU's justice commissioner, urged all 27 member states to hold their own national enquiries into clandestine CIA activities in Europe, and initiate criminal proceedings against those responsible.

"The governments need to reveal the truth, even if the truth is disturbing,” he told the Parliament, in a speech this morning.

If administrations are not in a position to act against their secret services, the European Commission, the EU’s executive arm, will “draw its own conclusions and come up with propositions,” particularly on “the role of intelligence services,” he added.

The CIA's practice of extraordinary rendition was first revealed in a Washington Post investigative article in November 2005. It involves the American transfer of untried terror suspects, or people suspected of having links to terror groups, to holding camps overseas for imprisonment or interrogation, with many flights needing to use European airports as stopovers.

Critics of the policy accuse the Americans of undertaking the action to avoid US laws forcing due process of suspects, and prohibiting torture.

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