A tropical storm killed at least 20 people in the Philippines, while nine people are still missing as huge amounts of rain that kept pouring down, causing major flooding and landslides, National Disaster Risk Reduction and Management Council chief Benito Ramos told reporters on Wednesday.

The storm called Nock-ten after a Laotian bird, was at first expected to cause more damage in the mountainous northern areas of the main island of Luzon on Wednesday.

The state weather also said the storm could bring heavy rain to Manila.

Nock-ten, first struck the eastern Philippines on Tuesday, killed at least 20 people, with another nine missing,

Five of the victims died as a landslide buried parts of their village and an estimated 645,000 people were also forced to flee their flooded homes in the coastal provinces of Albay and Camarines Sur in the southeast of Luzon, according to Ramos.

"Those two provinces are underwater," Ramos told AFP earlier.

He said the government was waiting for the skies to clear and the seas to calm down before sending emergency supplies by air and water to those provinces.

"We can't use the army trucks because the roads are flooded," he said.

The council said dozens of flights had been cancelled because of the storm.

Nock-ten had initially been expected to pass closer to Manila, the nation's capital, which has around 12 million people, and preventive measures were taken with schools closed across the city on Wednesday as authorities warned the inhabitants they should prepared for heavy rains.

Ramos said Nock-ten was following an erratic course but that according to the latest forecast Manila and other densely populous areas would not be affected by the bulk of the storm.

"It did not follow its projected track," he said.

Authorities however still warned that the new course of the storm could still put at risk the life of around four million people in mountainous areas of northern Luzon as landslides there remained a potential danger.

State weather forecaster Juanito Galang told AFP wind strength and rain volumes usually dissipated when a cyclone hit a wall of mountains, instead of going over flat land.

"But the danger there is, if rain falls on a mountaintop, it will rush down slopes. The tendency is for the water to go down as flash floods or cause landslides," Galang said.

"They're deadlier than ordinary floods because they occur suddenly and you are caught unaware," he said.

Ramos also warned that all areas within 500 kilometres (310 miles) of the eye of the storm, which includes Manila, should expect rain until it moved out to the South China Sea on Thursday.

An average of 20 storms and typhoons, some of them deadly, hit the Philippines every year. Storms killed 48 people on Luzon in May and June.

Unusually heavy rains also killed 42 people last month in the country's south, an area that is normally spared typhoons and storms.