More than 87,000 people were affected by the monsoon rains, which were made worse by Typhoon In-Fa even after it left the Philippines, the national disaster agency said on Sunday (July 25). At least 22,000 individuals are in evacuation centres, it said.
A 39-year-old woman in Baguio City, north of Manila, died from a vehicular accident caused by a fallen tree, the National Disaster Risk Reduction and Management Council said.
Its executive director Ricardo Jalad told a radio interview that the other two victims died after being hit by lightning.
Heavy rainfall hammered down on Metro Manila and many parts of the country this week, causing floods and displacing people in low-lying areas.
In some parts of the Philippine capital region, an urban sprawl of more than 13 million people, flood waters rose waist-high in places and cut off roads to light vehicles.
The Philippines, a South-East Asian archipelago of more than 7,600 islands, is hit by about 20 tropical storms a year but a warmer Pacific Ocean will make storms more powerful and bring heavier rain, meteorologists say.
The storms bring strong winds and heavy rains, resulting in flooding and landslides, significant damage to crops, houses and buildings, and deaths.
Between 2000 and 2016, natural disasters cost the Philippines US$20 billion in damage or an average of US$1.2 billion annually, according to an Asian Development Bank Institute paper.