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.
But some reports estimate that 80% of the capital is still under water.
The government has declared a "calamity" in Manila and 25 provinces, allowing access to emergency funds.
Some residents have emailed the BBC with their experiences. Lovely Lansang in Marikina says: "I am currently seeking refuge in a shopping centre. Many people are stuck either on their roofs or in the second storey of their houses due to the floods.
"The city is also without clean water and electricity. Right now, I am still in the shopping centre because the roads here are impassable," the email adds.
The equivalent of a whole month’s rain fell in six hours as Ketsana, also known as Ondoy, lashed the island of Luzon.
On Saturday, TV images showed gushing water turning roads into rivers, with floods chest-deep and rising.
Philippines President Gloria Arroyo appealed for donations and called for calm.
"I am calling on our countrymen, especially residents of metro Manila and other provinces in the path of the typhoon, to please stay calm, follow the instructions of local officials and civil defence authorities," she said in a TV message on Saturday.
Rizal Governor Casimiro Ynares was quoted by local media as saying other towns were completely inundated.
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 South China Sea on Sunday and Monday.