The 15-year-old male, named Arakan, was one of about 250 adult Philippine eagles remaining, according to the Swiss-based International Union for the Conservation of Nature, which lists the species as "critically endangered".
Days of non-stop rain caused the huge branch of a tree to fall on Arakan's cage at the Philippine Eagle Foundation's centre on the southern island of Mindanao, crushing the bird, on January 18.
Numerous large trees are planted inside the centre as the conservation group tries to simulate the eagles' natural habitat.
The eagle, also known as the monkey-eating eagle, is one of the largest birds of prey in the world and the most critically endangered of the raptors.
In October a juvenile male eagle was found dead, apparently shot, just two months after it was freed by the foundation.
Famed for its elongated nape feathers that form into a shaggy crest, the Philippine eagle is found only on four of the Philippines' largest islands but mostly on Mindanao and grows to one metre with a two-metre wingspan. The Philippine Eagle Foundation rescues stricken birds in the wild, including Arakan, who was turned over to the foundation in 1999.