More than 400 people have been killed and hundreds more were missing after a typhoon hit the southern Philippines, National Red Cross Secretary-General Gwendolyn Pang said on Saturday.

She said in a text message to Reuters that the death toll of 426 was expected to rise due to flash floods and landslides that forced tens of thousands to flee from their homes.

Typhoon Washi, with winds gusting up to 90km/hour, hit the resource-rich island of Mindanao late on Friday, bringing heavy rain that also grounded some domestic flights and left wide areas without power.

The Philippine National Red Cross (PNRC) said the death toll was caused by flash floods in Mindanao and another island. Soldiers and police were recovering more bodies washed ashore in nearby towns.

'The death toll might still rise because there are still a lot of missing people,' said Pang, adding that the hardest-hit areas were in the cities of Iligan and Cagayan de Oro.

Almost 400 people were unaccounted for, most of them from a coastal village in Iligan. Houses were swept into the sea by floodwaters while people were sleeping inside late on Friday.

Five miners were killed in a landslide in Monkayo on Mindanao and another 21 people drowned on the central island of Negros, the PNRC said.

The Philippines social welfare department said about 100,000 people were displaced and brought to more than a dozen shelters in Iligan and Cagayan de Oro.

Army spokesman Colonel Leopoldo Galon said search and rescue operations would continue along the shorelines in Misamis Oriental and Lanao del Norte provinces.

'I can't explain how these things happened, entire villages were swept to the sea by flash floods,' Galon said.

'I have not seen anything like this before. This could be worse than Ondoy,' he said, referring to a 2009 storm that inundated the capital, Manila, killing hundreds of people.

Television pictures showed bodies covered in mud, cars piled on top of each other and wrecked homes. Helicopters and boats searched the sea for survivors and victims.

'We ran for our lives when we heard a loud whistle blow and was followed by a big bang,' Michael Mabaylan, a 38-year-old carpenter, told Reuters. He said his wife and five children were all safe.

Aid worker Crislyn Felisilda said World Vision was concerned about children who became separated from their families or lost their parents.

'Many children are looking for their loved ones,' she said, adding children were 'crying and staring into space'.

Rescue boats pulled at least 15 people from the sea, another army spokesman, Lieutenant Colonel Randolph Cabangbang, told reporters.

Iligan City Mayor Lawrence Cruz said many people were caught by surprise when water rose one metre (three feet) high in less than an hour, forcing people onto roofs.

'Most of them were already sleeping when floodwaters entered their homes,' he said. 'This is the worst flooding our city had experienced in years.'

The national disaster agency said it could not estimate crop and property damage because emergency workers, including soldiers and police officers, were evacuating families and recovering casualties.

Six domestic flights run by Cebu Pacific were cancelled due to the rain and near-zero visibility in the southern and central Philippines. Ferry services were also halted, stranding hundreds of people.

An average of 20 typhoons hit the Philippines every year, often causing death and destruction.-Reuters