The report follows months of investigation by a special committee of MEPs led by an Italian, Claudio Fava.
"Many governments co-operated passively or actively (with the CIA)," said Mr Fava, quoted by AFP news agency.
He accused top EU officials including foreign policy chief Javier Solana of failing to give full details to MEPs.
The report echoed allegations made in June by the Council of Europe - Europe's leading human rights watchdog - that European states were complicit in illegal CIA operations as part of the US-led "war on terror".
The report says the US government had first informed EU member states in 2005 that it was using their territory to transfer terror suspects.
Over the course of three meetings with EU officials, "the Americans spoke in an explicit manner about the transfer system as a method in the fight against terrorism", Mr Fava told AFP.
The report speaks of at least 18 suspected CIA "extraordinary renditions" of terror suspects - the term used for transfers to third countries for interrogation.
They included the cases of a German, Khaled el-Masri - allegedly abducted in Macedonia and then detained in Afghanistan - and Egyptian former imam Abu Omar, allegedly kidnapped by CIA agents in Milan.
On Tuesday, a US court began to hear an appeal from Mr Masri after he lost an earlier lawsuit demanding damages and an apology from the US government.
Just like Maher Arar's lawsuit against the US government, Masri's will no doubt be dismissed over so-called 'national security concerns' which really means that the US government may never be held legally responsible, although Arar's lawyers are appealing the decision in his case.
That European countries willfully and knowingly participated in this monumental abuse of human rights shows just how far the callousness of Bush's policies extends. They should all be held to account.