The allegations have sparked a parliamentary inquiry after President Dalia Grybauskaite said she harboured "indirect suspicions" that such a facility existed.
According to unnamed former intelligence operatives quoted by ABC News, the CIA built the secret jail in 2004 and used it for more than a year, flying in at least eight suspected al-Qaeda terrorists from Afghanistan.

The high court today flatly rejected claims by
David Miliband, the foreign secretary, that releasing evidence of the
CIA's inhuman and unlawful treatment of UK resident
Binyam Mohamed would harm Britain's relations with the US by giving away intelligence secrets.
Evidence that the foreign secretary also wants to suppress is believed to reveal what British intelligence officers knew about Mohamed's treatment.
The CIA misled Congress about its torture program and other issues, the House Intelligence committee has concluded.
In a hearing of the House Intelligence committee this afternoon,
Reps. Anna Eshoo and Jan Schakowsky, both Democrats, pointed to at
least five instances going back to at least 2001 in which the C.I.A.
withheld information from or lied to Congress.
NEW YORK - A U.S. federal judge refused on Wednesday to release records describing interrogation techniques authorized for overseas use by the CIA, saying it was up to the agency to decide if they should remain secret.
U.S. District Judge Alvin Hellerstein ruled against requests by the American Civil Liberties Union to release documents from a total of 580 that included names and dates of when detainees were captured as well as descriptions of destroyed videotapes that showed CIA interrogations of two suspects.
MILAN - An Italian prosecutor called on Wednesday for 26 Americans, all but one believed to be members of the CIA, to be jailed for between 10 and 13 years each for the kidnapping of a terrorism suspect in 2003.
Public Prosecutor Armando Spataro also asked a Milan court to sentence four Italians, including the former head of Italy's Sismi secret service, to up to 13 years in prison for the abduction of Muslim cleric Hassan Mustafa Osama Nasr.
WASHINGTON - Seven former CIA directors asked President Barack Obama on Friday to quash a criminal probe of harsh interrogations of terror suspects during the Bush administration.
The CIA directors, who served both Democratic and Republican presidents and include three who worked under President George W. Bush, made their request in a letter sent Friday to the White House.
WASHINGTON - The Central Intelligence Agency is refusing to make public hundreds of pages of internal documents about the agency's defunct detention and interrogation program, saying such disclosures would jeopardize national security by revealing classified intelligence sources and operations.
NEW YORK - Did physicians and psychologists help the U.S. Central Intelligence Agency develop a new research protocol to assess and refine the use of waterboarding or other harsh interrogation techniques?
This is the question being raised in a new report by a leading human rights organisation. The group says that, if confirmed, it would likely constitute a "new, previously unknown category of ethical violations committed by CIA physicians and psychologists".
On this one-way planet of ours, it’s hard sometimes to imagine things any other way, but for a moment let’s try. Imagine, for instance, that in recent years the director of Iranian intelligence oversaw a program of
“extraordinary rendition” aimed at those who were believed to be prepared to commit acts of terror against that country’s fundamentalist regime.
Blackwater, the private mercenary company owned by Erik Prince, has been
thrust back into the spotlight by a series of stunning revelations about
its role in covert US programs. Since at least 2002, Blackwater has
worked for the CIA in Afghanistan and Pakistan on "black" contracts. On
August 19, the
New York Times revealed that the company was, in
fact, a central part of a secret CIA assassination program that Dick
Cheney allegedly ordered concealed from Congress.