Six people were killed and crew from two local boats were missing at sea as Tropical Storm Sarika headed out of Philippine waters Friday with many communities still flooded, rescuers said.

Four people drowned in the major southern island of Mindanao earlier this week while a boy died after falling into a swollen creek in Batangas city near Manila, and a woman drowned on the central island of Tablas, they said.

A coastguard plane on Friday found a number of people wearing orange life vests floating at sea off the main island of Luzon, said the government's National Disaster Risk Reduction and Management Council.

The survivors are believed to be among the 26 crew members of a 45-tonne fishing boat that went missing during the storm on its way to its home port from the Spratly islands, said the council's executive director Benito Ramos.

"The pilots saw some people afloat. We just don't know how many," Ramos told reporters. "The understanding is that since the boat was not found, it could have sunk," he said.

Philippine navy and coastguard vessels have been dispatched to the area off Anda town to pick up the presumed survivors, he added.

In another incident, one crew member of a barge went missing as the vessel, which was carrying agricultural products, ran aground near the town of Sariaya, south of Manila, the council said.

Several hundred people remained at evacuation centres across Luzon early Friday while waiting for floodwaters to recede, the disaster council said in its latest update.

Sarika was heading for southeastern China with peak winds of 65 kilometres (40 miles) an hour, after brushing the west coast of the main Philippine island of Luzon, the state weather service said.

An average of 20 storms and typhoons, some of them deadly, hit the Philippines every year.

Last month, tropical storm Aere left 31 people dead before Typhoon Songda killed another three.