The OV-10 Bronco, used largely as a maritime patrol support aircraft, failed to return to an air strip on the western island of Palawan last night, air force spokesman Lieutenant Colonel Miguel Okol told AFP.
"Combined elements of the coastguard and the navy have found parts of the debris and it appears to be the rear cargo compartment of the vessel," Okol said.
"We are still holding out hope that the two pilots were able to eject... We are searching for them."
"At this point, we could not yet speculate as to what exactly happened," he said, adding the weather was clear.
The crash is the latest in a string of deadly accidents involving surplus and often old foreign aircraft acquired by the Philippine military.
The air force's fleet of 30 Broncos were acquired from the United States in 1991 and Thailand in 2004.
Developed in the 1960s as a counter-insurgency aircraft by the US Air Force, the Broncos can carry heavy ammunition for a few hours in the air.
However, they are also used to monitor the archipelago's extensive coastal areas, as well as for search and rescue missions in the disaster-prone Philippines, he added.
Okol would not say exactly how old the crashed plane was, but insisted that all of the Broncos were in good condition.
"They have received a good number of upgrades, and we maintain them very well," he said.
The Philippine military is among the most poorly equipped in the region, and past modernisation efforts have consisted mostly of surplus hardware acquired from its traditional ally, the United States.
In 2010, eight air force personnel and a civilian were killed when a light cargo airplane crashed in the southern city of Cotabato.
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