Widespread flooding due to unusually heavy rains in many parts of the Philippines has killed 14 people in recent days, the government said Wednesday.

A total of 10 people drowned in villages lining the Pulangui, one of 11 rivers on the major southern island of Mindanao that overflowed their banks, the National Disaster Risk Reduction and Management Council said.

In two other incidents on Mindanao, a girl drowned in Cotabato city and a man was killed by the overflowing Lanang River, the government agency said in its latest report.

Two other deaths were reported on the main island of Luzon.

Large areas of Mindanao recorded more than two and a half times the normal level of rainfall in the first half of June, said Edna Juanillo, a climatologist at the state weather service.

"This is quite abnormal," she told AFP.

The floods began two weeks ago and affected 59 Mindanao towns and five cities with a combined population of more than 700,000, the disaster council said.

They wrought 429 million pesos' ($9.9 million) worth of damage to houses, crops, roads, bridges and schools, and have caused nearly 9,000 people to flee their homes to seek shelter in government-run evacuation camps.

The government has also handed out food and other relief aid to nearly 90,000 more people who chose to stay with relatives instead of going to the camps, it added.

More than 1,000 soldiers, government workers and volunteers have been clearing tonnes of water hyacinth from the Rio Grande river over the past week to ease flooding in Cotabato and surrounding towns, it said.

The council also reported flooding on some areas of Luzon, including parts of Manila, caused by a storm that brushed past the east coast on Monday.

It said two girls drowned in Dinalupihan, north of the capital, while a boy was missing in the partially flooded northern city of Olongapo.

The state weather service said it was monitoring a tropical depression off the Pacific coast that was expected to brush past eastern Luzon over the next few days.