Thousands of people were forced to flee their homes and take refuge in evacuation centres as rising waters reached the rooftops of one-storey buildings in some areas, civil defence officials said.
On Saturday, it rained 42 centimetres in Manila in just six hours, more than the entire average for the month of September.
Reporting from Manila's airport, Al Jazeera correspondent Marga Ortigas said shops that had stayed open for stranded commuters were rapidly running out of food and water.
She said: "We've been here now for almost eight hours - thousands of people are stuck here just as we are.
"All the roads in the city are blocked and vehicles are unable to come and pick up any passengers.
"Thousands of commuters are trapped in their cars on the roads and have been there since early afternoon."
'Stay on roof'
Power was cut in many parts of Manila due to flooding and protective measures being taken to prevent people from being electrocuted by fallen lines.
Gilberto Teodoro, the Philippines defence secretary who is also in charge of civil defence operations, said all the efforts of the police and the military were being concentrated on rescuing people trapped on rooftops.
But he said flooding in the streets and large numbers of stalled vehicles were hampering rescue workers trying to reach those affected.
He said in a radio broadcast: "If you are on the roof, don't try to leave. Just remain there on the roof and we will do everything to rescue you".
He said he had been forced to swim through chest-deep waters to reach his own office.
The storm, gusting up to 100km per hour, hit the main island of Luzon near the town of Infanta at about 0200 GMT on Saturday, moving west at 19km per hour, the national weather station said.
It has now returned to the sea and is heading towards Vietnam.
Gener Quitlong, a government weather forecaster, said: "We knew there would be rain, but not like this."
|Some children caught in the flooding were put in inner tubes and dragged to safety [AFP]
Local officials made radio appeals asking rescue agencies to send rubber boats to rescue stranded people, some of whom had spent the day on the rooftops of their homes.
At least four hospitals in the capital were forced to move their patients to higher floors after water began seeping into lower levels.
Residents in a flooded suburb of Manila rescued children from rooftops by placing them in inflated inner tubes before dragging them to higher ground.
One of the three airport terminals in Manila was forced to cancel and divert flights after flooding damaged its electrical system.
The storm is expected to move west across the main island of Luzon before exiting the country early on Sunday.