The CIA has run more than 1,000 flights within the European Union since 2001, often transporting terror suspects for questioning overseas, MEPs have said.
Kidnapping has "clearly" happened, the report says
The MEPs began a probe after claims the US flew suspects to secret prisons in countries that regularly use torture.
The US admits some terror suspects were flown overseas for interrogation, but denies sending them for torture.
Report author Claudio Fava said many EU states had ignored the hundreds of CIA flights that had used their airports.
Mr Fava, an Italian socialist MEP, singled out Sweden, Italy and Bosnia, which is not an EU member, for particular criticism.
A string of former detainees have come forward with stories alleging kidnap and transport by the US for interrogation in third countries - a process known as "extraordinary rendition".
Some have provided detailed accounts of alleged torture carried out in secret prisons outside EU or US jurisdiction.
Earlier this year the European human rights watchdog, the Council of Europe, made similar allegations, but these were dismissed by the US as hearsay.
Unveiling his report, Mr Fava said European governments and intelligence agencies should have verified the purpose of the CIA flights.
"We just have to think about the use of the airspace and airports by [the] CIA: more than 1,000 flights run by the US secret services, often used directly for extraordinary renditions," he said.
He suggested that flight plans and airport logs meant it was hard to believe that many of the stopovers were simple refuelling missions.
"The CIA has, on several occasions, clearly been responsible for kidnapping and illegally detaining alleged terrorists on the territory of [EU] member states, as well as for extraordinary renditions," said Mr Fava.
He made specific reference to several alleged abductions, including the snatch in Milan of Egyptian cleric Abu Omar in 2003.
Italian authorities were highly likely to have known the details of Abu Omar's case, Mr Fava said.
Investigators used data from Eurocontrol, the EU's air safety agency, to examine records of thousands of flights.
Mr Fava described many of the flights as "quite suspect".
Condoleezza Rice has denied the US would ever condone torture
Among those highlighted was the flight transferring Khalid al-Masri, a Kuwaiti-born German national, who was seized in Macedonia and transported to Afghanistan in 2004.
That plane flew from Algeria to Majorca, Spain, then to Skopje, Macedonia, and onto Kabul via Baghdad - all within 48 hours.
"They are rather strange routes for flights to take. It is hard to imagine... those stopovers were simply for providing fuel," said Mr Fava.
Mr Masri has previously given details of his transfer to the European Parliament. He alleges he was seized in Macedonia, interrogated in Kabul and released into Albania.
Mr Fava's committee spent more than three months interviewing top EU officials, magistrates, human rights activists and people who said they were abducted by the CIA.
Despite knowing that allowing rendition and possibly torture would breach a raft of European human rights treaties, Mr Fava said EU diplomats did nothing.
He singled out Italy, Sweden and Bosnia as governments he expected knew more than they made public about the flights.
Mr Fava's committee did not report on secret prisons, but he said members planned to visit countries such as Romania and Poland for further investigations later this year.
The CIA declined to comment on Mr Fava's findings.