The eaglet, which has yet to be named, is the first of its kind to be born at a conservation centre in the southern Davao province in two years.
Thirty four eagles, including the hatchling, are currently being kept in a massive cage at the centre.
Only about 600 of the species are thought to be left in the wild.
Considered to be the country's national bird, the Philippine eagle has been classified as "critically endangered" because of the loss of its natural rainforest habitat and hunting.
The Philippine Eagle Foundation called the baby bird "a breakthrough" for their breeding programme with curator Anna Mae Sumaya said that the birth "gives hope" for the native population.
"At two days old, this baby eagle can already lift its head and get food from forceps. It's also very active, attentive and observant of its surroundings," Ms Sumaya said in a statement.
In August, a rare eagle named Pamana was shot dead just two months after it was released into the wild following treatment for a previous gunshot wound.
Under Philippine law, killing a rare eagle is punishable by up to 12 years in prison and a fine of up to 1m pesos ($21,200; £14,000).
Source: bbc.com
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