It said 14 EU member states, including Ireland, allowed the US to forcibly remove terror suspects by permitting planes operated by the CIA to use their airspace and land at their airports.
The report condemned the countries involved for turning a blind eye to the operations.
In a statement, the Minister for Foreign Affairs said he was disappointed with the committee's report and that it had been obsessed with political point scoring.
Dermot Ahern said the alleged figure of 147 flights said to have passed through Irish airports was grossly inflated and pointed out that he had received categoric assurances from the US that no prisoners had been transferred through Ireland.
The report, which was carried out by a temporary committee, was approved by 382 MEPs, with 256 voting against.
The practice known as extraordinary rendition involves the transfer of terrorist suspects to other countries.
The report said the United States had operated 1,200 flights, flying suspects on to states where they could face torture.
The parliament voted to accept resolution condemning member states who accepted or ignored the practice.
