The deluge, the worst since 2009 when hundreds died in rampaging flash floods, was set off by the seasonal monsoon that overflowed major dams and rivers in Manila and surrounding provinces.
The capital and other parts of the country already were saturated from last week's Typhoon Saola, which battered Manila and the north for several days before blowing away Friday. That storm was responsible for at least 53 deaths.
"It's like a water world," said Benito Ramos, head of the government's disaster response agency. He said the rains flooded 50 percent of metropolitan Manila on Monday evening, and about 30 percent remained under waist- or neck-deep waters Tuesday.
He urged residents in areas prone to landslides and floods to stay in evacuation centers. Because the soil is saturated, even a little rain could be dangerous, he added.
"Now that it's getting dark, I would like to repeat, if the rains are heavy you should be at the evacuation centers," he said, warning that rescue operations are more difficult at night and could put responders at risk.
Manila's weather bureau said a tropical storm off eastern China had intensified monsoon rains in the Philippines, which were forecast to last until Thursday.
In Manila's suburban Quezon City, a landslide hit a row of shanties perched below a hill, burying nine people, according to Ramos.
Army troops and police dug frantically to save those buried, including four children, as surviving relatives and neighbors wept. All the victims were recovered, some whose bodies were found near an entombed shanty's door as they apparently tried to flee.
"My wife, children and grandchild are down there," a drenched Jessie Bailon told The Associated Press while watching rescuers dig into a muddy mound where his shanty once stood.
National police chief Nicanor Bartolome went to the scene and ordered all other slum dwellers to be evacuated from the still-soggy area.TV footage showed rescuers dangling on ropes to bring children and other residents to safety from flooded houses across the city. Many residents trapped in their homes called radio and TV stations desperately asking for help.
"We need to be rescued," Josephine Cruz told DZMM radio as water rose around her house in Quezon City, saying she was trapped in her two-story house with 11 other people, including her 83-year-old mother. "We can't get out because the floodwaters are now higher than people."
ABC-CBN TV network reported receiving frantic calls from people whose relatives were trapped in the deluge, many without food since Tuesday morning. They included a pregnant woman with a baby who wanted to be rescued from a roof and about 55 people who scrambled to the third floor of a Quezon city house as water rose below them.
Vehicles and even heavy trucks struggled to navigate water-clogged roads, where hundreds of thousands of commuters were stranded. Many cars were stuck in the muddy waters.
The government suspended work and classes Tuesday and Wednesday. Some shopping malls opened with limited grocery supplies that were quickly picked up by shoppers waiting in long lines.
The La Mesa dam, which supplies water to the capital of 12 million people, spilled excess water early Tuesday into the rivers flowing into Quezon City, as well as the neighborhoods of Malabon, Valenzuela and Caloocan, where several villages were submerged.
Along the swollen Marikina River, nearly 20,000 residents have been moved away from the riverbanks but many others asked to be rescued. Mayor Del de Guzman pleaded for patience and said overwhelmed rescue teams would try to reach everyone.
President Benigno Aquino III called an emergency meeting of Cabinet officials and disaster-response agencies. He ordered officials to make sure all residents were accounted for in flooded villages and discussed how flooded hospitals could be helped in case they were hit by power outages.
The Philippine Stock Exchange in the flooded financial district of Makati was closed. Also closed was the U.S. Embassy along Manila Bay in the historic old city, which was flooded last week when a storm surge pushed the water over the seawall.
In 2009, massive flooding spawned by a typhoon devastated Manila and surrounding areas, killing hundreds. The state weather bureau said that the current flooding was not as severe and that the weather may start to improve later this week.
Associated Press writers Jim Gomez, Teresa Cerojano and Oliver Teves contributed to this report.