Deputy intelligence chief Mustafa Noah was kidnapped outside Tripoli airport on Sunday.
Libya’s government is struggling to keep order as rival militias and hardline parties refuse to disarm two years after they helped oust Muammar Gaddafi in a NATO-backed uprising.
The state of emergency was declared in the city after at least one person was killed and dozens wounded in another wave of violence on Saturday.
The unrest began in the capital on Friday. More than 40 people were killed and another 400 were wounded.
Due to the situation in Tripoli, some of the streets in the city were blocked off.
Local residents formed protection brigades by their houses in order to ensure safety from the militias, the medics added.
Libyan Prime Minister Ali Zidan has appealed for restraint, stating that “the coming hours and days will be decisive for the history of Libya and the success of the revolution.”
On Saturday, thousands of protesters gathered to remember those who died in Friday’s clashes, as the government declared three days of mourning. Zidan also demanded that all armed militias leave Tripoli “without exception.”
“The existence of weapons outside the army and police is dangerous,” he said. “All armed militias need to leave Tripoli, without exception.”
Friday’s clashes began as thousands of protesters gathered in Tripoli on Friday, calling to intensify the security presence and end the militias’ rule which was established in 2011.