Philippine authorities warned on Monday an intensifying storm could bring more misery to the flood-battered capital and surrounding areas, where nearly half a million were in evacuation centres.

While flooding that covered 80 per cent of Manila last week had largely subsided, vast areas of mainly rice-growing provinces to the north were still under water that in some places remained neck-deep.

Most of the 411,000 people crammed into gymnasiums, schools and other government evacuation centres were in the flooded farming provinces, with many others struggling by living in partly submerged homes.

"These are the people we are most worried about," civil defence chief Benito Ramos told AFP.

"We have not yet fully recovered and here comes another storm."

Two weeks of relentless monsoon rains peaked early last week with about two days of torrential rain across the main island of Luzon, claiming at least 92 lives and affecting more than 3.4 million people, according to the government.

Manila, a megacity of about 15 million people, endured its worst flooding since 2009, while farmers to the north said they had not experienced waters reaching such levels for decades.

The farming regions are a natural catch basin, with rivers streaming down from mountains to the north eventually ending in Manila Bay.

But many of the dams in the mountains were already close to overflowing before last week's deluge, while the natural drainage areas near the bay have been getting increasingly clogged with millions of people living around them.

With the waters not yet receding, Tropical Storm Kai-tak was approaching from the east on Monday and was expected to start dumping up to 3.5 centimetres (1.3 inches) of rain an hour in the evening, the state weather bureau said.

While not being as directly impacted, Manila was also expected to suffer more heavy rain as the storm compounded typical monsoon weather, it said.

"The ground is already wet and saturated, and we could have landslides and flash floods," Science and Technology Secretary Mario Montejo, who oversees the weather bureau, told reporters.

On the outskirts of Manila, flood survivors were still struggling to clean up their homes and even just to get food, after losing most of their belongings last week.

"I hope to God this new storm doesn't happen," said 64-year-old grandmother Fe Bermejo as she queued alongside hundreds of other people for Red Cross relief goods in Valenzuela, one of the hardest hit coastal districts.

In the neighbouring district of Malabon, people were trickling back to clean up their mud-streaked homes amid warnings to be prepared for fresh evacuations.

"Many have returned to their homes to rebuild, but sadly they may have to leave again if there are more floods because of this new storm," said Roderick Tongol, head of Malabon's disaster response unit.

"We are on heightened alert, and we have placed all our rescue teams on standby."

The National Disaster Risk Reduction and Management Council said that, of the more than 3.4 million people affected by the floods, one million were forced to flee their homes.

The government has admitted to being overwhelmed by the scale of the relief effort, with access to toilets at evacuation centres and getting relief goods to the homeless a major problem.

The Philippines is hammered by an average of 20 storms a year, many of them deadly.

But Environment Minister Raman Paje said much more intense rains, such as those experienced last week, should be considered the 'new normal' as part of climate change.