The government declared Manila and numerous provinces to be in a "state of calamity," Defence Secretary Gilberto Teodoro said, as heavy rains brought by the storm caused the worst flooding seen in the capital in some 20 years.
Government weather forecaster Gener Quitlong said the equivalent of one month's worth of rain fell on the city in less than a day.
"We knew there would be rain but not like this," Quitlong told reporters.
One of the three airport terminals in Manila was forced to cancel and divert flights after the flooding hampered its electrical system.
Local officials interviewed on radio said they were moving to evacuate more of their residents.
Huge traffic jams clogged the roads in the capital as floodwaters caused many vehicles to stall.
Local officials made appeals on air, asking rescue agencies to send rubber boats to rescue stranded people.
In a suburb of Manila, residents in a flooded area were seen rescuing children from rooftops by placing them in inflated inner tubes before dragging them to higher ground.
The second level of a three-step storm alert was raised over the eastern provinces of Luzon while the first level alert was hoisted over metropolitan Manila and surrounding areas, the government said.
The storm is expected to move west, across the main island of Luzon, before exiting the country early Sunday.
An average of 20 typhoons and storms enter the Philippines from the Pacific Ocean over the eastern seaboard every year.