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Mustafa Noah, who overseas the intelligence agency’s espionage unit, was kidnapped as he emerged from Tripoli airport after returning from a trip to Turkey, two security sources have confirmed.
His abduction comes amid renewed political instability and a spike in violence as the government attempts to crack down on a number of armed militia groups.
On Friday, 45 people were killed in Tripoli, the health ministry says, when a militia group opened fire on protesters who approached their headquarters demanding they leave the capital.
A militia spokesperson said that protesters were armed and fired first.
The fighting spread on Saturday east to the suburb town of Tajoura, where local militia clashed with fighters from the city of Misrata, 200km east of Tripoli.
Libyan Prime Minister Ali Zeidan called the killing of what he said were unarmed protesters a crime, and urged militia fighters to leave the capital.
In early October, Zeidan himself was abducted from his residence at the Corinthia Hotel in the city centre by an unknown number of armed men but was released a few hours later.