The national disaster agency said 14,023 people, most of them from a flood-prone Manila suburb, had moved into evacuation centres.
"We ask residents of affected areas to remain alert and vigilant, take precautionary measures, and cooperate with their respective local authorities," presidential spokesperson Harry Roque said in a statement.
Harsh weather has hit several parts of the world in recent weeks, bringing floods to China, India and Western Europe and heat waves to North America, raising new fears about the impact of climate change.
The Philippines, a Southeast Asian archipelago of more than 7,600 islands, sees about 20 tropical storms a year but a warmer Pacific Ocean will make storms more powerful and bring heavier rain, meteorologists say.
In some parts of the Philippine capital region, an urban sprawl of more than 13 million people, flood waters, in places waist-deep, cut off roads to light vehicles.
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