Foreign Office said that the special aircraft C-130 carrying the body of the ambassador left Islamabad for Manila after a guard of honour ceremony was held at Nur Khan Airbase in Rawalpindi to pay respect to the envoy.
Federal Minister of Commerce Khurram Dastgir Khan and an officer from the Ministry of Foreign Affairs accompanied senior officials of the Philippines and family member of the late ambassador on the special plane.
The envoys of the Philippines and Norway and the wives of the Malaysian and Indonesian ambassadors were among seven persons killed when Mi-17 helicopter, carrying 12 foreigners, crashed in Pakistan-occupied Kashmir's Gilgit-Baltistan area in the north on May 8.
Diplomats from about 30 countries along with their families were going to Naltar on a three-day excursion for sight-seeing and participate in the inauguration of a chairlift at a ski-resort which Prime Minister Nawaz Sharif was scheduled to unveil when one of the aircraft made crash landing.
The Taliban had claimed responsibility for the downing of the chopper and said Sharif was their target.
Pakistan Army, however, has ruled out the possibility of any terrorist or subversive activity in the crash and said the chopper crashed due to a technical fault while landing.