Kadhafi was kidnapped on Friday by an unknown armed group in Lebanon's eastern Bekaa valley, but was freed by police several hours later and taken in for questioning, security sources said.
Today he was interrogated for more than three hours by judicial investigators, who charged him with "withholding information on the disappearance of Shiite imam Mussa Sadr".
Sadr went missing in 1978 during an official visit to Libya, along with an aide and a journalist.
Kadhafi's lawyer Shadi Hussein, speaking to AFP outside the courtroom, said the Libyan businessman was charged because "the crime is still ongoing, since those kidnapped" remain missing.
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"And because the charged man is one of the sons of the main accused in this case, Moamer Kadhafi," Hussein added.
According to an AFP journalist at the scene, Kadhafi had two black eyes and was limping.
His medium-length hair was slicked back, and he was allowed to speak to his Lebanese wife Aline Skaf by phone for a few minutes, although her location was not disclosed.
Bekaa is an eastern stronghold of the Lebanese Shiite movement Hezbollah.
The lavish lifestyles of Kadhafi's family and entourage helped fuel the anger in Libya that sparked the protests that led eventually to the strongman's ouster and killing in 2011.
That year, as the dictator was battling the uprising against him, a private jet carrying Skaf was refused permission to land at Beirut airport.
An official said at the time that acting transport minister Ghazi Aridi had asked for a detailed passenger manifest and that his request was rejected by the Libyans.
Three more were killed during the Libyan revolt.