The security documents show intimate links between the CIA and Gadhafi's ousted regime, including intelligence-sharing and handing over suspected terrorists to Libya for interrogation.
One notable case is that of the new opposition military commander in Tripoli, Abdel-Hakim Belhaj, who says he was tortured by CIA agents at a secret prison, then returned to Libya.
Two of the documents discovered in the abandoned security building appear to be American correspondence to Libyan officials in March 2004 to arrange Belhaj's rendition.
The documents say he would be flown from Malaysia to Libya, and asks for Libya government agents to accompany him, as well as requests American "access to [Belhaj] for debriefing purposes once he is in your custody," according to the AP.
The document reportedly says the Americans wanted assurance that he would be treated humanely and his human rights would be respected.
CIA spokeswoman Jennifer Youngblood told the AP that "it can't come as a surprise that the Central Intelligence Agency works with foreign governments to help protect our country from terrorism and other deadly threats," but declined to comment on any specific allegation related to the documents.
This latest discovery opens a window into the West's efforts to turn Libya's leader from foe to ally, and provides new details about the depth of the Bush adminsitration's involvement with authoritarian governments in the war on terror, revelations that could spark tensions between Washington and the new Libyan leaders who have pushed Gadhafi out of power in hopes of creating a new government for the country.