"Concealing the truth"
The document echoed charges from the Council of Europe's human rights body that European states were complicit in US rights abuses during the Bush administration's so-called "war on terrorism".
"At least 1,245 flights operated by the CIA have flown into the European airspace or stopped over at European airports," the draft said.
The draft, presented on Tuesday to the EU assembly's special committee investigating alleged CIA kidnappings and prisons in Europe, called on national authorities to launch separate legal probes into claims about whether their national security services were involved and whether state authorities violated EU human rights laws.
The report said 11 EU nations - Britain, Poland, Italy, Germany, Sweden, Austria, Ireland, Spain, Portugal, Greece and Cyprus - had knowledge of the US secret anti-terror measures taking place on European soil.
It said the committee had obtained "serious circumstantial evidence" showing that Poland may have hosted a temporary secret detention centre for the CIA.
No EU governments have admitted that the alleged anti-terror operations were carried out on their soil.
"Concealing the truth"
Governments have been warned by Franco Frattini, the EU justice and home affairs commissioner that if they were found to have known of the CIA renditions and secret flights they could face lawsuits for violating EU law.
Fava said that "almost all the member states" apart from Germany and Spain had failed to co-operate fully with his investigation.
The draft report also singled out the former head of Italy's SISMI intelligence service, accusing him of "concealing the truth" when he told the committee that Italian agents had played no part in the CIA kidnapping of an Egyptian cleric in 2003.
On the contrary, SISMI officials played an active role in the abduction of Abu Omar from Italy, and the CIA kept Italian authorities informed on his later detention in Egypt, the report said.
It said Abu Omar had been "held incommunicado and tortured ever since".
US acknowledges renditions
The US has acknowledged using renditions, or secret transfers of suspects, between countries.
George Bush, the US president, confirmed in September that the CIA had held high-level terrorism suspects at secret overseas locations.
The EU and Council of Europe inquiries were launched partly in response to press reports that the US ran secret prisons in Poland and Romania. Both countries have denied the allegations.
Tuesday's report complained of lack of co-operation from the Polish government and regretted Romania's "lack of willingness to investigate in depth".
Over six months, the parliamentary commission took evidence from 130 people including government officials, secret service agents, judges, lawyers, journalists and NGO representatives.
Members of the investigating commission also travelled to the United States, Britain, Germany, Poland, Portugal and Macedonia.
A parallel enquiry is being carried out by the 46-nation Council of Europe.
Its rapportuer Dick Marty in June accused 14 nations of involvement in CIA secret flights and, in the cases of Poland and Romania, of housing clandestine detention centres.