Libyan deputy intelligence chief Mustafa Nuh has been kidnapped, security sources have told the BBC.
Local media say he was abducted from Tripoli airport, but the government says it is unable to confirm this.
This comes Tripoli observes a general strike in protest against the presence of militia groups in the city.
The strike was called after more than 40 people died in two days of clashes. Militia units from the city of Misrata have now been ordered to leave Tripoli.
The order to withdraw within 72 hours came in a statement issued by Misrata's local council and the council of elders. One Misrata commander later confirmed to the BBC that his brigade would comply.
Libya's weak central government has struggled to keep control amid powerful local militia.
These groups were originally formed to help oust Col Muammar Gaddafi, but two years later they refuse to disarm.
No group has said it abducted Mr Nuh, but militias have seized senior officials before to get political leverage.
Prime Minister Ali Zeidan was held hostage for several hours by gunmen in October, before being released unharmed.
The Libyan capital has been tense and volatile since the clashes on Friday between militia based in Tripoli and protesters trying to evict them from their headquarters.
Tripoli's local council has declared a three-day general strike, calling on all militia groups leave the area.
The BBC's correspondent in Tripoli, Rana Jawad, says most shops and schools are closed and many roadblocks have been erected by local residents and various armed groups.