The pan-European body's Secretary-General, Terry Davis, on Wednesday announced "a formal inquiry into recent reports suggesting that terrorist suspects may have been secretly detained in or transported through a number of... member states with the possible involvement of foreign agencies".
The council's member-states would have until 21 February next year to provide information to the inquiry, Davis said in a written statement on Wednesday.
The inquiry would look at governments' compliance with European human rights law and whether officials had been involved in "unacknowledged" detentions or transport of detainees, including "at the instigation of any foreign agency", the statement said.
Press reports have said Washington's Central Intelligence Agency (CIA) has operated secret detention facilities in Eastern Europe, Afghanistan, Thailand and elsewhere in order to circumvent US laws protecting detainees, particularly restrictions on the use of torture.
Planes allegedly operated by the CIA have been spotted at airports in Finland, Germany, Hungary, Iceland, Italy, Poland, Portugal, Romania, Spain and Sweden as well as Morocco.
Britain, the current chair of the European Union, said on Tuesday that following requests from several member states it would seek answers from Washington to allegations that the CIA had held terrorist suspects in Europe.
Planes allegedly operated by the
CIA have been spotted in Europe
The Council of Europe's parliamentary assembly had already announced a probe into reports of the CIA operating clandestine detention facilities in some European countries.
The new probe announced on Wednesday came amid a flurry of fresh reports on alleged covert flights.
In Vienna, Austrian Air Force chief Erich Wolf confirmed that a Hercules aircraft, suspected of transporting prisoners for the CIA, had flown through Austrian airspace in 2003. The aircraft's owner, Tepper Aviation, has insisted the flight was a civilian one.
In Lisbon, Focus magazine published photographs taken by an aviation buff showing what the magazine said were CIA planes linked to the transport of terror suspects making stopovers at Portuguese airports in March and May.
The magazine said one of the planes had touched down at Tires airport near Lisbon while the other three landed in Portugal's mid-Atlantic Azores archipelago where the United States has a military base.
Reacting to that report, both Foreign Minister Diogo Freitas do Amaral and Defence Minister Luis Amado reiterated that no CIA planes had made stopovers in Portugal, at least since the current government came to power in March.
"I can categorically affirm that Spanish laws have not at any time been violated"
US Ambassador to Spain
In Helsinki, meanwhile, the Borgaabladet daily newspaper said a Hercules plane, possibly used by the CIA to transport terrorist suspects, had landed at Vantaa international airport in May 2003 before carrying on to Stockholm.
While the Finnish Foreign Ministry said it could not confirm the reports, civil aviation authority spokeswoman Irmeli Paavola told the STT news agency the aircraft was not one of five linked by various media to the CIA.
In Madrid, US Ambassador Eduardo Aguirre responded to questions about alleged CIA prisoner flights stopping over in Spain by insisting that no Spanish legislation had been broken.
"I can categorically affirm that Spanish laws have not at any time been violated," Aguirre told journalists on Wednesday.
The Council of Europe, based in Strasbourg and a separate institution from the European Union, comprises 46 countries. It focuses on issues of human rights and democracy.