The prime minister's office said in a statement that it had lost contact with Mohamed Ali Ghatous, who works for Prime Minister Ali Zidan, and was searching for him. Officials said he went missing late Sunday and his car was found on the side of the road on the outskirts of Tripoli the next day.
The officials say he may have been abducted, speaking anonymously in line with regulations.
Two years after the country's civil war, Libya is struggling to build a unified army and police force and reign in militias, which include many rebels who fought to oust the country's longtime dictator Moammar Gadhafi. The government often depends on the militias to fill the security vacuum.
Recently, militias have taken offense at statements by ministers criticizing the near impunity they enjoy in many parts of the country and suggesting they needed to be brought under control.
Ghatous' disappearance comes less than a week after Zidan was besieged in his office by militiamen who demanded his ouster over remarks he made threatening to summon outside help to confront the armed groups.
On Sunday, the same day that Ghatous disappeared, dozens of militiamen surrounded the Justice Ministry in a daylong siege and also called for minister Salah al-Marghani's resignation.
Al-Marghani had told a Libyan TV station that some of the militias were illegitimate and were operating illegal prisons. He demanded that they relinquish control over them to the Justice Ministry.
Zidan and al-Marghani also held a joint news conference on Sunday, saying that militias would be held accountable for any attacks.