"As soon as it heard the reports, the Libyan government contacted the US authorities to demand an explanation."
US special forces seized Abu Anas al-Libi in a commando raid in broad daylight on Saturday, sealing a 15-year manhunt for the top al Qaeda suspect.
A source close to Libi said he was snatched by armed men in Tripoli.
Libi, who was on the FBI's most wanted list with a $5 million reward, was indicted in US federal court in New York for allegedly playing a key role in deadly 1998 bombings of US embassies in Kenya and Tanzania.
"As the result of a US counterterrorism operation, Abu Anas al-Libi is currently lawfully detained by the US military in a secure location outside of Libya," Pentagon spokesman George Little said in a statement.