Tropical Storm Ketsana triggered the worst flooding in decades in the capital Manila and nearby provinces.
Defence Secretary Gilbert Teodoro said troops, police and civilian volunteers had rescued more than 4,000 people - many clinging to each other on roofs.
More than 250,000 have been driven from their homes, officials say.
Eighty percent of the capital is still under water.
The government has declared a "calamity" in Manila and 25 provinces, allowing access to emergency funds.
Roads leading into Manila were rendered impassable by stalled vehicles, and some ferry services were cancelled.
The Philippines chief weather forecaster has blamed climate change for the downpours that saw 40cm (16in) of rain fall on Manila in a single day.
Thousands of passengers were stranded as international and domestic airports were shut down.
Ketsana, with winds of up to 100km/h, is expected to head out over the East Sea on Sunday and Monday.
Add new comment