Thousands of people displaced by floods triggered by tropical storm Fung-Wong returned to their mud-caked homes in the Philippine capital of Manila, as the death toll from the disaster rose to five.

Heavy rains had paralysed the sprawling metropolis of more than 12 million people, as well as nearby regions, with roof-high floods causing 83,000 people to leave their homes, according to the National Disaster Risk Reduction and Management Council.

"We have no choice but to come back. We can't afford to rent an apartment," butcher's wife Lovi Barbosa, 35, told AFP as she attempted to remove dirt from the floor of her home near a still swollen creek.

She said she and her five children, aged between two and 10, spent a sleepless night sitting on the ground outside a tyre repair shop because the local school was already full of similarly displaced neighbours.

Three weeks' worth of rain swamped the region on Friday, state meteorologists said, as the eye of the relatively weak storm brushed past the northern tip of the main island of Luzon, more than 400km away.

The state weather service said Fung-Wong was forecast to hit Taiwan on Sunday. 

Many of the areas hardest hit by floods, such as Barbosa's neighbourhood, are shantytowns illegally occupying the banks of rivers and other waterways.

"Generally, the floods have already subsided. People are starting to return to their homes," Alexander Pama, executive director of the disaster council, said Saturday.

The bad weather left five people dead and one missing, he told a news conference. 

The storm itself caused power outages across northern Luzon, while rough seas left a small ferry off the central port of Cebu badly damaged on Friday, Pama added.

Navy rescuers along with nearby commercial ships retrieved 31 people from the stricken vessel, Philippine Navy spokeswoman Commander Marineth Domingo told AFP.

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.

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.

Taiwan has readied nearly 50,000 troops in preparation for the storms arrival.

Three counties in southern Taiwan have decided to close offices and schools from Saturday night while dozens of flights and ferry services were suspended, authorities said.

Uni Air, which cancelled 12 domestic flights Saturday, announced that it will suspend all services scheduled for Sunday.

The defence ministry said it has ordered 48,000 soldiers to be on stand-by in preparation of the storm while the authorities urged people in low-laying areas to take precautions against flooding as the storm is expected to generate torrential rains across the island.