The CIA ran secret prisons in Poland and Romania from 2003 to 2005 to interrogate high-level detainees in its war on terror, a Council of Europe investigator said in a report released today.

Dick Marty said that he now had enough evidence to state that alleged detention centres definitely existed, and that the “highest state authorities" in the countries involved knew of their existence, including the presidents, national security advisers and defence secretaries.

Leading terror suspects Abu Zubaydah and Khalid Sheikh Mohammed were among those to be secretly held and interrogated in Poland, said the report, citing unnamed CIA sources.

In response, the European Commission today called on EU member states accused of hosting secret CIA prisons to hold urgent, independent investigations and ensure that victims were compensated.

Friso Roscam Abbing, a Commission spokesman, told a news briefing that the European Union executive was “very concerned indeed” about Mr Marty's report.

He said that the Commission considered “extraordinary rendition” - the extra-judicial capture and secret transfer of suspects to countries where they may face torture - was illegal under EU law and harmed the fight against terrorism.

In his report today, Mr Marty claimed that after 9/11 the CIA set up a programme to “kill, capture and detain" so-called high value terror suspects. The collaboration of friendly foreign governments was critical to the secret detention programme.

The operation took place within the framework of Nato’s security policy, after Nato and the United States reached a secret deal in 2001 allowing the CIA to run covert prisons in Europe, he claimed.

“The secret detention facilities in Europe were run directly and exclusively by the CIA,” said the report.

“While it is likely that very few people in the countries concerned, including in the governments themselves, knew of the existence of the centres, we have sufficient grounds to declare that the highest state authorities were aware of the CIA’s illegal activities on their territories.”

In Poland these included the former president Aleksander Kwasniewski, Marek Siwiec, national security chief, Jerzy Szmajdzinski, the defence minister, and the head of military intelligence Marek Dukaczewski.

In Romania, he named former president Ion Iliescu, President Traian Basescu, national security advisor Ioan Talpes, defence minister Ioan Mircea Pascu and the head of directorate for military intelligence Sergiu Tudor Medar.

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