A US civil liberties group is suing a subsidiary of Boeing for allegedly helping the CIA fly suspects to secret overseas jails where they were abused.
The CIA is believed to have flown more than 1,000 flights over Europe
The American Civil Liberties Union (ACLU) has filed the lawsuit against Jeppesen Dataplan on behalf of three men allegedly abducted by the CIA.
The Bush administration acknowledges its policy of "extraordinary rendition" but denies any suspect is tortured.
Jeppesen has said it cannot confirm whether or not the CIA is a customer.
A spokesman for the Colorado-based firm told the BBC News website: "We have thousands of customers who fly tens of thousands of flights every day and with each one of them they have a reasonable expectation that their operations will be kept confidential."
A report approved by a European Parliament committee earlier this year said more than 1,000 covert CIA flights had crossed European airspace or stopped at European airports in the four years after the 9/11 attacks.
The ACLU's lawsuit, filed in California, accuses Jeppesen of knowingly providing direct flight services to the CIA that enabled the clandestine transfer of the three suspects to foreign prisons.
The cases involve the alleged abuse of Binyam Mohamed, an Ethiopian citizen currently held in Guantanamo Bay; Elkassim Britel, an Italian citizen now held in Morocco; and Ahmed Agiza, an Egyptian citizen taken from Sweden to Egypt where he remains in jail, the ACLU says.
It claims Jeppesen, through the travel service provided by Jeppesen International Trip Planning, has been a "main provider of flight and logistical support services for aircraft used by the CIA in the US government's extraordinary rendition programme".
These services include preparing route, weather and fuelling plans for flight crews, gaining over-flight and landing permits, and facilitating customs clearance, the ACLU says, as well as providing security for crews and aircraft.
Since December 2001, Jeppesen has provided flight and logistical support to a total of 70 rendition flights made by at least 15 aircraft, it concludes.
"American corporations should not be profiting from a CIA rendition programme that is unlawful and contrary to core American values," Anthony Romero, executive director of the ACLU, said in a statement.
The US administration has faced criticism from legal experts and human rights activists over its policy on detentions of terrorism suspects.
US President George Bush admitted in September 2006 that terror suspects had been held in CIA-run prisons overseas, but he did not say where the prisons were located.
He said no detainees were now held under the CIA programme and that the CIA treated detainees humanely.