Tropical Storm Kai-tak blew out of the Philippines on Thursday, offering some relief for millions of people struggling to recover from a brutal few weeks of monsoon rains that claimed 109 lives.

However civil defence chief Benito Ramos said floods could still hit the Cagayan river basin, a farming region of more than two million people as runoff from storm-induced rains descend from surrounding mountain ranges.

"The storm is gone but we're still on red alert. In 10 hours we'd know how much water would descend onto the Cagayan river," Ramos told AFP.

Kai-tak swept across the Philippines' main island of Luzon on Wednesday, dumping heavy rain on the Cagayan basin and other areas in the north, leading to the deaths of four people.

But the storm also caused more bad weather in other parts of Luzon, including the capital Manila and surrounding farming regions where an intense deluge triggered by another storm caused devastating floods last week.

Those floods, which came after nearly a fortnight of relentless rain that soaked the ground and filled rivers, killed at least 105 people, according to the government's latest tally.

The government's National Disaster Risk Reduction and Management Council said it was still providing relief aid to nearly a million people impacted by last week's floods, including more than 216,000 at evacuation centres.

Floods that persisted in the farming provinces surrounding Manila had started to recede, and the number of people in evacuation centres was about half the peak over the weekend.

Ramos said he expected most people would be able to return to their flood-damaged homes within a week.

However he said more than 12,000 families, or about 60,000 people, had lost their homes completely and would need temporary shelters for a longer period.

Anna Lindenfors, country head for aid group Save the Children, warned that the millions of people affected by the floods faced months of miserable and dangerous conditions either inside or outside evacuation centres.

"The need is massive and urgent -- millions of people are suffering the miserable consequences of these floods and we must try to reach them before the rains hit again," she said in a statement.

Kai-tak strengthened into a typhoon Thursday and was heading towards the coast of southern China west of Hong Kong.