Heavy rains paralysed the sprawling metropolis of more than 12 million people and nearby regions yesterday, with roof-high floods chasing 83,000 people from 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.
Three weeks' worth of rain swamped the region yesterday, state meteorologists said, as the eye of the relatively weak storm brushed past the northern tip of the main island of Luzon, more than 400 kilometres (250 miles) away.
The state weather service said Fung-Wong was forecast to hit Taiwan tomorrow.
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Many of the areas hardest hit by floods, such as Barbosa's neighbourhood, are shantytowns illegally occupying the banks of rivers and other waterways.
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, 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.
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.