The 77-page report condemned 14 EU members for their involvement in the practice of what the U.S. government calls rendition -- secretly moving suspects to other countries for interrogation.
The report said the union "condemns extraordinary rendition as an illegal instrument used by the United States in the fight against terrorism," which many center-right members objected to, the EU Observer reported.
The vote on accepting the report after amendments was 382 in favor, 256 against and 74 abstentions.
Some parts of the report were toned down, including some criticism of the British and German governments, the Observer said.
The report claimed there had been "at least" 1,245 CIA flights using European airspace and also criticized several member states for refusing to cooperate with the committee's investigation.