Typhoon Pablo (international codename: Bopha)killed at least 52 people in the Philippines on Tuesday, officials and television reports said as the strongest storm to hit the country this year wreaked devastation.

ABS-CBN television said 43 of the deaths occurred in one southern town that was in the direct path of Pablo's 210 kilometre (130 mile) an hour winds soon after it hit land on Mindanao island's east coast at dawn.

"I've counted 43 bodies on the floor," reporter Vina Araneta told the station by telephone from a government building that she said had been converted into a temporary mortuary in New Bataan town.

The military said a landslide destroyed a Philippine Army patrol base in a mountainous area of the town, while a local official said an army truck laden with soldiers and civilians was swept away in a flash flood.

Neither the civil defence office in Manila nor the armed forces could give official confirmation of the 43 reported deaths, saying their rescuers were having a hard time reaching the remote town.

Officials said there were nine confirmed deaths, all but one of them occurring on Mindanao island in the country's south. Three of the victims were crushed by falling trees.

Four fishermen were also reported missing off Mindanao's east coast, said Freddie Bendulo, planning and development officer of Davao Oriental province.

By early evening a weakened Pablo was streaking across the Sulu Sea, having changed course westward in the afternoon after briefly threatening the central tourist islands of Bohol, Cebu and Negros, the state weather service said.

The typhoon brought driving rain and strong winds, toppling trees and power lines, causing localised flooding and forcing more than 56,000 to seek refuge in emergency shelters according to a civil defence office update.

Winds blew roofs off some buildings and residents of coastal and low-lying communities in Mindanao moved into shelters as floods hit some areas, residents and AFP reporters said.

Television footage showed logs being swept down Mindanao's Sumilao river, and utility workers cutting up fallen trees that were blocking highways.

They also showed large numbers of people lying on mats and cardboard sheets on the concrete floors of gyms turned into temporary shelters.

A total of 146 flights to and from Mindanao and the central islands had been grounded since Monday night and more than 3,000 ferry passengers were stranded as vessels were ordered to stay in port, according to the civil defence update.

Large parts of Mindanao, which is not normally hit by typhoons, were still without electricity on Tuesday night, it said.

People living in the path of the storm did what they could to protect their homes and possessions.

"We have taken our pigs and chickens inside our house because their shed might be destroyed," said shopkeeper Marianita Villamor, 46, from the southern farming town of San Fermin.

In Cagayan de Oro city, where giant waves crashed down on the shoreline, mayor Vicente Emano said on ABS-CBN television that police rounded up all residents of low-lying areas and moved them to government shelters.

In Tagum city, hotel waiter Edgie Atilano, 23, said he and his family hunkered down in their home as Pablo bore down.

"At 3:00 am, we were woken by strong rain and howling winds. Trees and branches started snapping off near the house," said the father-of-two.

"This is my first time to experience a strong typhoon. It was a bit scary."