The government estimates that 26,000 Filipinos were working in Libya before the uprising against Moamer Qadhafi broke out, part of a vast number of mostly lower-paid migrant workers in the country from across Asia and Africa.
The Filipinos' jobs ranged from domestic helpers to engineers and white-collar workers.
More are expected home in the coming days, some evacuated by their employers and others helped by the Philippine government, Malaya said.
At the airport, the first repatriated Filipinos, most of them construction workers, profusely thanked their recruitment agency for helping them leave, before they were taken to a holding area to meet their families.
The new arrivals complained about not being able to make phone calls out of Libya but did not appear troubled by their experience.
"We are making arrangements for the availability of ferries to take our nationals out to Malta or Crete as well as making arrangements for possible shuttle flights to take them out from Tripoli," Malaya said.
Newly-appointed Philippine foreign secretary Albert del Rosario has also departed for Tunisia to help facilitate the evacuation, he said.
Philippine diplomatic teams are currently deployed at the Egyptian and Tunisian borders with Libya and alternative land routes are being set up to help more Filipinos leave.
Of the total 26,200 Filipinos, about 13,000 are due to be taken out under the government's evacuation programme and the rest are expected to leave with their multinational employers.