In the densely populated capital, rescuers were deployed across the city on Wednesday to help evacuate people from low-lying homes after downpours turned streets into rivers.
People clutched flimsy umbrellas as they waded through thigh-deep murky water or used small boats and shopping trolleys to move around.
Government offices were shut and classes suspended, while more than 70 domestic and international flights were cancelled because of the weather.
“Many areas are flooded so we have rescuers deployed all over the city. There is an overwhelming number of people asking for help,” said Peachy de Leon, a disaster official in suburban Manila.
The typhoon, which has swept past the Philippines as it heads towards Taiwan, intensified the southwest monsoon rains typical for this time of year, the state weather forecaster said.
“Usually the peak of rainy season is July and August and it so happens that there is a typhoon in the eastern waters of the Philippines that enhances the southwest monsoon,” said senior weather specialist Glaiza Escullar.
More than 200mm (8 inches) of rain fell in the capital in the past 24 hours, Escullar said, which was “not unusual”.
That takes the death toll from heavy rains over swaths of the country to at least 12 since Tuesday, as tens of thousands sheltered in evacuation centres.
Taiwan closed schools, suspended the stock market, and declared a typhoon holiday on Wednesday as Gaemi barrelled towards the island, bringing torrential rains and whipping winds to its northeast.
The storm is expected to make landfall in northeastern Taiwan by 10pm (14:00 GMT) and President William Lai Ching-te urged everyone to “put safety first” during a morning emergency briefing.
Authorities evacuated more than 2,100 people living in precarious conditions in three northern regions, particularly Hualien, a mountainous area with high risk of landslides.
Trains and ferry services were suspended and more than 250 international flights were cancelled on Wednesday.
