The ministry announced a "mandatory" evacuation of all 13,000 of its nationals living in Libya last month after the beheading of a Filipino construction worker abducted by unknown suspects.
That killing was followed by the gang rape of a Filipina nurse in the capital Tripoli on Wednesday.
"Our target is 100 percent" evacuation, foreign department spokesman Charles Jose told AFP on Friday.
Foreign Secretary Albert del Rosario left for Tunisia to arrange the evacuations on Thursday.
He announced the government would charter ships to pick up Filipinos from Libyan ports, or transport them by land if the sea vessels failed to gain passage.
But many Filipinos in Libya fear losing their jobs, del Rosario has said.
Jose added that only a fraction had fled since the government's initial warning for Filipinos to leave Libya was issued two months ago.
"We've had that advisory (for Filipinos to leave Libya) for two months, but less than a thousand have come home. Can you just imagine the challenge we're facing?" Jose said.
The Philippines previously launched a mass evacuation of its workers in Libya in 2011, when most of the 30,000 Filipinos there left during the violent chaos leading to the toppling of the late dictator Moamer Kadhafi.
Jose said about 4,500 returned to the Philippines in repatriation flights paid for by the government at that time.
Others were evacuated by their employers and international aid organisations.
However, about 1,600 Filipinos, mostly doctors and nurses, remained in Libya throughout the 2011 upheaval, according to government data.
Their numbers later increased after the Philippines lifted its travel ban for workers to go to Libya in March 2012.
That ban was re-imposed on May 30 this year, when the government also strongly advised all Filipinos already in the country to leave, using their own resources, as security conditions deteriorated.
The mandatory evacuation announced last month puts the onus on bringing them home on the Philippine government.
Jose said del Rosario had arrived in Tunisia on Friday but had yet to update the foreign office in Manila about the chartered vessels.
About 10 million Filipinos work around the world, earning more money in a wide range of skilled and unskilled sectors than they could in their impoverished homeland.