The 15-year-old male bird, 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 in the southern island of Mindanao, crushing the raptor on January 18, the foundation said.
The eagle, also known as the 'Monkey-eating Eagle', is one of the largest birds of prey in the world and is the most critically endangered of all the world's raptors, the IUCN says on its website.
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 a metre (3.3 feet) with a two-metre wingspan.
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The eagle, which is the country's national bird, is protected by law but authorities say the biggest threat is the loss of its habitat as humans encroach on the country's dwindling forest ranges.
Efforts to release rehabilitated birds into the wild have had mixed success.
In October last year, a juvenile male eagle was found apparently shot to death just two months after it was freed by the foundation.