At least four people drowned after heavy flooding in large areas of the rain-soaked Philippines, authorities said Thursday, with some of the waters up to chest height.

Over-flowing rivers swamped coastal population centres on the major southern island of Mindanao, causing all the known fatalities, rescuers said, and Manila was also under threat.

The National Disaster Risk Reduction and Management Council in the capital said 19 towns were under floodwater after heavy rains driven by a storm began falling on Monday.

"The water in some parts were chest-deep," said Nasser Mastura, vice governor of Maguindanao province that is among those heavily inundated.

"We have removed thousands to safer grounds," he said on local television, without giving exact numbers.

The government declared a school holiday in Manila and in some nearby suburbs Thursday, while a number of domestic flights to tiny provincial airports were either delayed or cancelled due to the stormy weather.

The La Mesa dam, Manila's lone tap water reservoir, was about to overflow, triggering official warnings that nearby residents could be asked to evacuate if the heavy rains continued.

"We are expected to have continuing heavy rains today until late tomorrow," said Robert Sawi, a senior state weather forecaster.

He said the rains were caused by a tropical depression at sea to the southwest of the main island of Luzon.

The weather disturbance was however not likely to develop into a full-blown typhoon and was forecast to blow off toward southern China by Friday, he said.