Rescue workers in trucks and rubber dinghies plucked residents from the tops of flooded homes, after one of Manila's major rivers burst its banks, swamping heavily populated eastern districts.
"We're dealing with floods over a large area. Our local as well as national responders are out there leading the rescue operations," Mina Marasigan, spokeswoman for the National Disaster Risk Reduction and Management Council told AFP.
She said the first known fatality was a girl who drowned at a flooded slum in northern Manila.
However it brought heavy downpours of more than three weeks' worth overnight Thursday across Manila, more than 400 kilometres to the south, state weather forecaster Gener Quitlong told AFP.
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The hardest-hit area appeared to be the Marikina river valley in eastern Manila, where brown, swiftly flowing water rose at least a storey high on heavily populated communities near its banks.
Rescuers aboard rubber dinghies, some motorised and some powered by paddles, plucked people from flooded homes, an AFP reporting team saw.
Two soldiers involved in the rescue sat on the bonnet of a stranded military truck that appeared to have been disabled, while the roofs of cars and other smaller vehicles bobbed above the floodwaters.