Typhoon Pablo a killed at least six people in the Philippines on Tuesday as the strongest storm to hit the country this year forced more than 50,000 to seek refuge in emergency shelters, officials said.

Pablo made landfall on the island of Mindanao in the south of the country at dawn, bringing driving rain and packing gusts of up to 210 kilometres (130 miles) an hour that toppled trees and brought down power lines.

Six people were killed, including an elderly woman who was crushed to death when a tree fell on her house, rescue officials said, without identifying the other five or saying how they had died.

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

By early afternoon, the typhoon had slowed and weakened somewhat with top gusts of 195 kilometres an hour, the state weather service said.

Civil defence chief Benito Ramos said the storm had altered course and was expected to hit the central islands of Bohol, Negros and the popular tourist resort island of Cebu later on Tuesday.

Hundreds of people are killed each year by the 20 or so tropical cyclones that hit the Philippines, but Ramos said the low casualties so far from Pablo were down to government efforts to move people to safety.

"So far, casualties have been minimal. We attribute this to the cooperation of our people and the efforts of local officials," he told reporters.

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

More than 53,000 people had moved into nearly 1,000 government shelters by early Tuesday, the civil defence office said.

A total of 145 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, the civil defence office said.

Large parts of Mindanao, which is not normally hit by typhoons, were without electricity after power was cut to reduce the risk of fires and electrocutions, said Liza Mazo, a regional civil defence official.

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," 46-year-old shopkeeper Marianita Villamor from the farming town of San Fermin on Mindanao's east coast told AFP by telephone.

Villamor said her relatives who lived in a nearby coastal area had joined hundreds of other families who moved into temporary shelters including schools and other government buildings late Monday.

In Tagum, a city of 243,000 people, hotel waiter Edgie Atilano, 23, said he and his family hunkered down in their home as Bopha 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, who added that nearby roads were blocked with fallen trees.

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

The commercial centre of Cagayan de Oro, a city of 600,000 people, was hit by flooding as rivers overflowed.

City mayor Vicente Emano said on ABS-CBN television that police rounded up all residents of low-lying areas Tuesday and moved them to government shelters.

"There were people who refused to leave their homes yesterday. Now those areas are under code red (flood risk) so I ordered the police to go and force them to leave because these areas could soon be flooded," Emano added.