Philippine Department of Foreign Affairs spokesman Charles Jose told AFP "(The) reason for staying is mainly economic," adding that "4,000 still remain".
Libya has been wracked by conflict for the past four years, with rival governments and powerful militias now battling for control of key cities and the country's oil riches.
Three Filipino oil workers are still missing and are believed to have been taken captive at work following an attack by gunmen in early February, Jose said.
The government and private employers have since brought thousands of Filipinos home, but others have resisted, lured by salaries they could not expect in the Philippines.
Many of them are medical workers who make up the backbone of Libya's hospital staff and are being offered financial incentives to stay.
About 10 per cent of Filipinos work overseas, attracted by higher salaries than they can earn at home. Their remittances are a major pillar supporting the country's economy.