The facilities were shut down after media reports of their existence, ABC News reported on Monday, citing current and former CIA agents.
Eleven al-Qaida prisoners who were held in Eastern Europe were relocated "to a CIA site somewhere in north Africa", ABC reported citing CIA sources.
The US scrambled to get all of the suspects off European soil before US Secretary of State Condoleezza Rice arrived in Europe on Monday, ABC said, citing the sources.
ABC said the CIA declined to comment, and an agency spokesman was not available when Reuters tried to contact him.
According to ABC News, eight top al-Qaida figures and three others were held at one time at a former Soviet air base in Eastern Europe, and some were later moved to a second country.
ABC said Polish sources had identified a base as the site of one of the secret prisons.
Thailand has been named as one
of the CIA secret prison sites
US-based Human Rights Watch has said Poland and Romania were the most probable locations for the detention centres, but both countries have denied it.
The US has neither confirmed nor denied the existence of the secret prisons, which the Washington Post first reported on last month.
In an expanded report on its website, ABC News cited sources directly involved in setting up the CIA secret prison system as saying that it began with the capture of Osama bin Ladin lieutenant Abu Zubayda in Pakistan.
ABC said Abu Zubayda was first held in Thailand in an unused warehouse on an active air base.
The report said after Abu Zubayda recovered from life-threatening wounds, he was made to stand long hours in a cold cell and strapped feet up to a "water board" until he begged for mercy and began to cooperate.
In "water-boarding," a detainee is strapped down, dunked under water and made to believe that he might be drowned.
Before leaving Washington for Europe on Monday, Rice defended US treatment of terrorism suspects. She did not directly address the allegation that the CIA has run secret prisons in Eastern Europe. However, she reaffirmed that the US does not use torture.
ABC News cited intelligence officers as saying that Rice could say that because of a presidential finding that approved "enhanced interrogation techniques," which the US has said are not torture. These include sleep deprivation and water-boarding.
Ramzi bin al-Shaiba is one of the
9/11 accused now in CIA custody
ABC cited its sources as saying that the al-Qaida suspects being held are regularly subjected to these interrogation techniques.
In the report on the website, ABC cited sources as saying that of the suspects held by the CIA, only one, Ramzi bin al-Shaiba, a suspected coordinator of the 11 September 2001 attacks, did not require water-boarding before he talked.
The report said al-Shaiba broke down in tears after he was walked past the cell of Khalid Shaikh Muhammad, the mastermind of the attacks on the US.
The sources were cited as saying a visibly shaken al-Shaiba started to cry and became cooperative.