"To ensure the safety and security of the Philippine military troops deployed to conflict-affected areas, the country's contingents in the Golan Heights and Liberia are scheduled to be repatriated within the year," a Defence Department statement said.
"The 331-strong Filipino contingent serving as part of the United Nations Disengagement Force (UNDOF) in the Golan Heights will be repatriated at the end of their tour of duty in October," the statement said.
"The Philippines prioritises the safety and security of its troops, but remains committed to the peacekeeping missions of the United Nations," the statement said.
Defence Department spokesman Peter Paul Galvez said the Philippines would not send back its troops to the Golan Heights "unless the situation improves".
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He expressed confidence the pullout would not hurt the country's standing with the United Nations, recalling that Filipino troops had remained in the Golan Heights in 2013 even after Australian, Croatian and Japanese peacekeepers were withdrawn.
Galvez also said that the Filipinos from Liberia would be quarantined for at least 21 days after arriving to ensure they are not infected.
Foreign Department spokesman Charles Jose said "we don't expect this decision to affect our UN standing and international image," citing the country's involvement in peacekeeping operations for years.
Last year the Philippines also considered pulling its Golan peacekeepers out after 25 of them were kidnapped but later freed by Syrian rebels in two separate incidents.
Philippine President Benigno Aquino later agreed to a UN request to keep the Filipinos in the Golan after receiving pledges that they would be given more equipment to protect themselves.
The withdrawals would leave only 157 Filipino troops still serving as UN peacekeepers in Haiti, the armed forces said.