Amnesty says the report "exposes a covert operation whereby people have been arrested or abducted, transferred and held in secret or handed over to countries where they have faced torture and other ill-treatment."
The lengthy report tells of the experiences of three Yemeni men, who believe they were taken by US authorities to secret prisons, in journeys through what they felt were different time zones and climates.
It includes testimony taken in February and March from Muhammad Bashmilah, Muhammad al-Assad and Salah Nasser Salim Ali, also known as Salah Qaru.
Mr Bashmilah said he was detained in Jordan in October 2003 while on a trip to visit his mother.
Mr Ali said he was detained in Indonesia in August 2003 and then flown to Jordan where he was taken into custody.
While Mr Al-Assad said he was detained in Tanzania in 2003.
None of the men could identify where they were taken next.
Eastern Europe or central Asia
In their statements, the three describe, in detail, travel times, changing temperatures, and daylight hours, which Amnesty believes indicates the men may have been held in eastern Europe.
The men were allegedly held for 13 months at a so-called "black site," a secret facility believed to be run by the CIA, before they were returned to Yemen where they were charged with forging travel documents, Amnesty said.
In a statement released with the report, Amnesty International said the men’s stories raised "the possibility that they were held somewhere in eastern Europe or central Asia."
"Their captors went to great lengths to conceal their location from the men, but circumstantial evidence such as climate, prayer schedules, and flight times to and from the site suggest that they may have been held in eastern Europe or central Asia," Anne
FitzGerald, a senior adviser with Amnesty, said in the statement.
“But without further information from the US government and European authorities, it's impossible to verify exactly where."
The US government says any transfer of terror suspects is carrying out according to American and international law.
The CIA declined to comment on the report.
Renditions investigated
Investigations of the US’ so- called practice of “rendition”, where US operated flights allegedly transferred terror suspects to third countries for interrogation, are underway by the continent’s top human rights watchdog, The Council of Europe.
In their report, Amnesty claimed that the CIA was exploiting a loophole allowing private aircraft to land at foreign airports without having to inform local authorities - unlike government or military planes - and called for inspections of planes suspected of being involved.
"The CIA has exploited aviation practices that would otherwise require their flights to be declared to aviation authorities," the report says.
Amnesty claims it "has records of nearly 1,000 flights" by planes that appear to have been "permanently operated by the CIA through front companies" and most of which used European airspace.
"One particular aircraft is known to have made over 100 stops in Guantanamo Bay," it said. "Another took (suspect) Abu Omar to Egypt from Germany after he was kidnapped in Italy," Amnesty said.
Its Czech Republic branch says three planes made a total of 20 landings in the capital Prague as part of the program.
Amnesty International called on governments and the aviation industry to ensure the practice of rendition does not continue.