Bases handed over to the Ministry of Defense and the Libyan air force included an airbase and Islamic call center, CNN reported Thursday.
It was unclear where the groups would go. Other groups remain in Tripoli.
Government officials called the handover a major step in rebuilding Libya and its security forces.
During a news conference, Prime Minister Ali Zeidan bristled at a question whether the handovers were real.
"The weapons that were in the hands of these groups was the security threat and now this threat has disappeared," he said.
The Libyan public had become focused on the militias because the groups refused to disarm in the two years since the fall of Moammar Gadhafi.
Members of militias from the city of Misrata killed 47 demonstrators last week. More than 500 people were injured in the march on the militias' headquarters.
The Misrata militias withdrew this week.