The investigation, headed by Swiss Senator Dick Marty, says European nations "tolerated" or "colluded actively" in the rendition, abduction, and detention of terrorist suspects.
The report names former Polish President Aleksander Kwasniewski, as well as the former and current presidents of Romania, Ion Iliescu and Traian Basescu, and says they "could be held accountable" because they "knew about and authorized" the activities.
It says that two top Al-Qaeda terror suspects, including Khalid Sheikh Muhammad, the self-proclaimed mastermind of the September 11, 2001, terror attacks, were secretly held and interrogated in Poland.
It alleges that a secret agreement among NATO allies in 2001 provided the basic framework for these activities.
In the report, Marty also accuses Germany and Italy of obstructing his inquiry.
The report did not name its sources, but it said no conclusions were ever based on single statements.
In a statement, the Romanian Foreign Ministry dismissed the report, saying it lacks evidence and has "no degree" of credibility. A spokesman for Poland's Foreign Ministry said Warsaw maintains its position that "there were no secret centers in Poland."
The European Commission said the EU executive is "very concerned" about the report.
(with material from agency reports)