The single-prop SF-260FH was flying in formation with two other planes on a training flight when it crashed off Nasugbo township in Batangas province south of Manila, said air force spokesman Lt Col Enrico Canaya.
The planes also were taking part in activities commemorating the 70th anniversary of the liberation of the province from the Japanese toward the end of World War II, he said.
He said rescuers recovered the bodies of the pilot and the co-pilot about 300 metres from the shore.
Some of training planes have been modified for combat missions against insurgents.
The Philippines military, one of the most poorly-equipped armed forces in Asia, is dealing with Muslim extremist and communist insurgents as well as incursions from China into waters it claims in the disputed South China Sea.
It plans to acquire a dozen FA-50 fighter jets from South Korea to beef up its air force by 2017.