Parts of Manila were under six feet (1.8 metres) of floodwater on Saturday after heavy rain lashed the capital overnight, forcing more than 400 people to flee their homes, officials said.
There was also a strong typhoon lurking in the region, and although it was moving away from the Philippines and towards Japan, forecasters said it was adding to the wild weather.
“Typhoon (Sanba) has no direct effect but the storm enhanced the southwestern monsoon so we will continue to experience rains,” said government meteorologist Gary de la Cruz.
Low-lying coastal areas of the capital were hardest hit, forcing people to leave their homes, the National Disaster Risk Reduction and Management Council said.
At least 10 domestic flights were cancelled and universities in affected areas called off classes, the council said.
Although the heavy rain eased later in the day, de la Cruz said the Philippines could continue to suffer heavy downpours until Tuesday.
So far, Sanba has caused only one fatality in the Philippines, a fisherman who ventured out to sea on September 12 but whose dead body was recovered two days later, the disaster management council said.
Storms and flooding from torrential rain affected more than two million people in August and killed scores.
The Philippines endures about 20 major storms or typhoons each rainy season.