The committee, comprising 46 Euro MPs, will also probe whether European governments were aware of these alleged activities, and if citizens of the EU or of candidate states were involved, including as victims, in Europe or elsewhere.
It will submit "all necessary recommendations" to the EU Parliament and will work "as closely as possible" with other institutions working on the same subject, such as the Council of Europe, a pan-European rights body.
This report will be delivered within four months after it begins work, probably next week.
Washington has come under intense fire in the last few months from reports about hundreds of CIA flights, suspected of carrying undeclared prisoners across European airspace, since the 11 September, 2001 terror attacks.
The co-head of the EU parliament's Green group, Daniel Cohn-Bendit, said the new committee should not shy away from interviewing any potential witnesses, without discrimination, even, if it were necessary, "the Queen of England".
The temporary committee will have no power to force anyone to appear before it, according to the leader of the Socialist Group, Martin Shulz.
But by requesting individuals' attendance it will "send signals at the international level which will compel those invited to publicly justify any refusal", he added.
Specifically the EU assembly wants to know if CIA detention centres existed in Europe and whether the CIA had used European airports to transport terrorist suspects to places where they could face torture.
The EU move came as Scotland's main opposition party published a dossier implicating firms in helping what it alleged were US flights transporting terror suspects through Scottish airports.
The report by the Scottish National Party (SNP) lists planes, the dates on which they landed and 10 companies that have allegedly operated on behalf of the CIA.
At the weekend, a Greek newspaper reported that CIA aircraft "employed to transport Muslim detainees" repeatedly landed at Athens International Airport between 2002 and 2005.