Tens of thousands of people fled roof-high floods and one girl drowned in the Philippine capital on Friday as another vicious storm swept across the disaster-plagued country.

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'll stay awake for as long as we can. When the water gets here we have to run again," Mylene Reyes, 49, told AFP as she huddled on the damp floor of a gym crammed with 850 other evacuees in one of the worst-hit areas.

Reyes said she, her son and grandson fled their shanty a few blocks away before dawn. A short while later it was swallowed up by a nearby creek.

Street vendor Erma Jacob, 59, and her family sought refuge at a nearby school in the morning, leaving their stove, television set and electric fan on the roof of their flooded home without having anything to cover them.

"This is depressing, but we're used to it," said the woman, who said it was the third time the house was hit by floods since 2009.

An average of 20 typhoons or major storms hit the Philippines each year, killing hundreds and bringing misery to millions.

Super Typhoon Haiyan, bringing the strongest winds ever recorded on land, left 7,300 people dead or missing across the central Philippines in November last year.

The latest foul weather began pounding Manila, a megacity of more than 12 million people, on Thursday night as tropical storm Fung-Wong approached the main Philippine island of Luzon.

Fung-Wong's winds were relatively light, its peak winds slowing to 75 kilometres (47 miles) an hour at sea at 4:00pm (0800 GMT), four hours after it brushed past the northeast tip of the main island of Luzon.

However it brought more than three weeks' worth of rain overnight Thursday across Manila, more than 400 kilometres to the south, state weather forecaster Gener Quitlong told AFP.

Rain pummelled Manila throughout Friday, causing floods across the entire city, forcing all schools and government offices to close. More rain was forecast across Luzon into Saturday.

The first known fatality was a girl who drowned at a flooded slum in northern Manila, national disaster council spokeswoman Mina Marasigan told AFP.

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.

- Dramatic rescues -

Rescuers aboard rubber dinghies, some motorised and some powered by paddles, plucked people from flooded homes, an AFP reporting team saw.

People held on to lengths of rope to get to high ground safely and avoid being pulled by the strong currents, and the roofs of cars and other vehicles bobbed above the floodwaters.

The Marikina mayor, Del de Guzman, told local ABS-CBN television at least 27,000 of his constituents were evacuated.

In all, flooding had forced at least 50,000 people to flee their homes in and around Manila, Social Welfare Secretary Corazon Soliman said.

Ghelynne del Rosario saw their northern Manila family bungalow swamped by chest-deep floods after she, her mother, her grandmother in her eighties, and their three dogs sought refuge on the second floor of a neighbour's house.

"I am angry that I have to do this each time it rains hard," the Manila lawyer, 35, told AFP.

Major flooding hits Manila frequently, and residents typically blame bad drainage systems and other types of poor government urban planning for exacerbating the problem.

In September 2009, Tropical Storm Ketsana dumped a month's worth of rain across Manila in just six hours, unleashing the worst flooding in the capital in four decades and killing more than 460 people.

Manila airport authorities cancelled 21 domestic flights on Friday, with six international flights also diverted elsewhere in the country due to bad weather.