Officials reported at least three dead, 11 injured and four missing.
The dead included a 5-year-old boy whose house was hit by a concrete wall that collapsed. His two adult relatives also were injured.
Schools, offices, the stock exchange, courts and embassies were closed as the weather bureau placed metropolitan Manila -- a sprawling area of 12 million people -- under red alert. Officials from several flood-hit cities and provinces announced that classes would remain suspended Tuesday.
The flooding following a night of heavy monsoon rains, enhanced by Tropical Storm Trami. The storm hovered over the North Philippine Sea and drenched the main northern island of Luzon with up to 30 millimeters (just over an inch) of rain per hour.
Government weather forecaster Jori Loiz said as of late Monday, Trami was 580 kilometers (360 miles) east of northern Itbayat island, crawling eastward at 7 kilometers per hour (4 mph). It is expected to exit the Philippines by Wednesday or Thursday and move toward China.
He said heavy rains were expected to continue to drench metropolitan Manila and nearby provinces Monday night and advised residents in flood-prone areas to be on alert.
TV footage showed residents trapped on rooftops as raging floodwaters swept through Binan town on Lake Laguna, near Manila.
Flooding has become more frequent in Manila because of deforestation of mountains, clogged waterways and canals where large squatter communities live, and poor urban planning.
In the chilly northern mountain town of Sagada, army troops and police rescued 29 tourists, including 13 Japanese, who were stranded for several hours inside a cave after two days of heavy rains caused a stream at the entrance to swell, Office of Civil Defense official Andrew Alex Uy said. One Filipino tourist remained missing.
Several dams in Luzon were forced to open their flood gates because of rising waters and thousands of residents downstream were told to move.
A landslide and floods shut down traffic on a major highway leading out of Manila. In the outlying provinces of Cavite, Batangas and Ilocos Norte father north, local authorities said flash floods forced thousands to take refuge in schools and other sturdy buildings.
Forecasters said the storm was expected to strengthen as it slowly moves away from the Philippines.
The Philippine archipelago is among the most battered by storms in the world. About 20 tropical cyclones hit the country every year.
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