VILNIUS (Reuters) -- The U.S. Central Intelligence Agency (CIA) ran a secret prison in Lithuania where Al-Qaeda suspects may have been held, a parliamentary probe in the Baltic state has found.
The head of Lithuania's domestic intelligence agency has already resigned as speculation about secret jails has intensified.
U.S. broadcaster ABC News reported in August that Lithuania was the third European country, after Poland and Romania, believed to host secret CIA jails
Some CIA staff are reported to have said the use of overseas detention centers was designed to circumvent U.S. law.
Arvydas Anusauskas, the head of parliament's national security and defense committee, said the investigation found Lithuanian intelligence opened two detention centers in cooperation with the CIA.
"There were facilities, there were possibilities, there were [CIA] planes, though we can't know what was on board.... Therefore such a possibility exists," he said, when asked whether any CIA detainees were held in Lithuania.
Top officials were not informed about the jails, and there was no political approval, he said.
Prime Minister Andrius Kubilius said it was "a matter of great concern" that such infrastructure existed and that it could be possible to detain suspected terrorists without government control.
In a statement, he said he expected good relations with the United States to continue, but that a strategic partnership could not be an excuse for "Soviet methods, ignoring civilian control of the special services and in breach of existing laws."
ABC News said a secret CIA prison operated near Vilnius airport from early 2004 to late 2005 and that CIA planes flew into Lithuania with top level Al-Qaeda suspects.
Anusauskas told a news conference that CIA flights entered Lithuania but were not inspected, and it had not been possible to determine who had been on board.
The investigation was the second into the secret jail allegations, demanded by President Dalia Grybauskaite after an earlier probe found no evidence.
"It [the investigation] only proves suspicions she had for some time that there were premises designed for detention and there were flights which could have been used for transporting prisoners," said the president's spokesman, Linas Balsys.
"The president has no doubts that bilateral Lithuania-U.S. relationship cannot be overshadowed by these conclusions."
Last week, Grybauskaite said she had ordered the recall of Lithuania's ambassador to Georgia, Mecys Llaurinkus, who led the state security department from June 1998 until April 2004.
The investigation found that five planes linked to the CIA landed in Lithuania in 2003-06, and that domestic intelligence officials prevented customs and border guards inspecting them.
The U.S. Embassy in Vilnius declined to comment, saying it was U.S. policy not to comment on intelligence matters.