The carcass of the giant bird, belonging to a species that is threatened with extinction, was recovered from a resident of Gingoog city on the southern island of Mindanao, the Philippine Eagle Foundation said.
It had only been released into the wild by conservationists two months earlier.
"Minalwang (the name given to the bird by the foundation) was captured. The bird died of infection that had been aggravated by its captivity," the foundation's communications officer Beauxy Auxtero told AFP.
Auxtero said the Gingoog resident who had captured the bird had not been placed under arrest.
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The bird had two bullet wounds, Josie de Leon, wildlife resources division chief of the environment department's Protected Areas and Wildlife Bureau, told AFP earlier today.
Killing endangered species in the Philippines is punishable by a 12-year prison term and stiff fines, she added.
"Our people are gathering information on who might have killed it," de Leon said.
The foundation, a non-government outfit based in the Mindanao city of Davao, retrieved the bird from the resident and nursed it back to health.
The bird was fitted with a radio transmitter and let go at the Mount Balatukan natural park near Gingoog two months ago, the fifth Philippine eagle rescued by the foundation and released back into the wild, said Auxtero.
The Philippine eagle, found only on four of the Philippines' largest islands but mostly on Mindanao, grows to a metre (3.3 feet) with a two-metre wingspan.