A late-season storm expected to be the last of the year in the Philippines has killed 11 people but spared a southern region where more than 1,000 died in a powerful typhoon early this month, officials said.

The national disaster agency said three people were killed when a tree fell on their house in Eastern Samar province, where Tropical Storm Wukong made landfall on Christmas Day (local time).

Other deaths occurred due to drowning and landslides as the storm slashed through central islands.

The storm weakened into a low pressure area over the South China Sea off Palawan province, southwest of Manila.

"The worst is over," Civil Defence chief Benito Ramos said.

Officials said heavy rain on mountains surrounding Kalibo, the capital of Aklan province on Panay Island, caused a river running through the city to overflow and triggered a flash flood late Wednesday.

No casualties were reported but many houses near the river were damaged, said Efren Trinidad, assistant to Kalibo Mayor William Lachica.

The flooding was aggravated by the high tide, preventing the river from emptying into the sea, Trinidad said.

He said canals were blocked by heavy silt brought down from nearby hills.

The city is the gateway to the famous island resort of Boracay, which was not affected.

"As we were conducting rescue operations, flights were coming in because the weather was fine. The moon was shining while we were being flooded. It was ironic," Trinidad said, explaining that rains fell mostly over the mountains.

It was the 17th storm to hit the country this year. Forecasters said no other disturbances were expected through the end of the year, which also marks the end of the rainy season.

Typhoon Bopha lashed the main southern island of Mindanao early this month, killing at least 1,067 people and leaving more than 800 missing.

It triggered flash floods laden with mud, boulders and uprooted trees that rampaged through farming communities, wiping out entire villages.

The typhoon caused nearly 37 billion pesos in damage to agriculture, property and infrastructure, making it one of the worst storms to hit the country in recent years.

- AP