Terming the abductions "a violation of international laws", Foreign Secretary Albert de Rosario said he would recommend to President Benigno Aquino for withdrawal of the over 300 Filipinos peacekeepers in the region.
Del Rosario said that Philippines was cooperating with the international partners "for early and safe return" of the abductees.
A total of 843 Filipinos are serving as peacekeepers at various locations at present, he said.
The government has already repatriated 4,000 Filipinos from strife-torn Syria and is working to bring to safety other undocumented national working there, he said.
The move comes as countries which contribute troops to the UN Disengagement Observer Force (UNDOF) have expressed renewed concern about security in the zone between Israel and war-stricken Syria.
UNDOF, monitoring a ceasefire between Israel and Syria since 1974, has about 1,000 peacekeepers and civilian staff from Austria, India, Morocco, Moldova and the Philippines.