The Philippines prepared for mass burials of flood victims on Monday to minimise health risks from rotting cadavers after a cyclone disaster left hundreds dead or missing on Mindanao island.

Hard-pressed authorities in the port cities of Cagayan de Oro and Iligan, where villagers were swept to sea as they slept in coastal slums, are struggling to cope with the devastation left by tropical storm Washi.

The Philippine Red Cross put the death toll at 652 with 911 others listed as missing on Monday but national government officials said the figures for the missing may have been overstated in the post-disaster chaos.

"Today we will dig a mass grave and bury the unclaimed bodies as well as those in an advanced state of decomposition," Iligan's Mayor Lawrence Cruz said on national television.

Up to 50 of about 300 bodies recovered in Iligan since Washi struck in the early hours of Saturday will be communally buried, possibly during the day, so that they do not pose a health risk, Cruz said.

Television footage from an Iligan mortuary showed a corridor lined with bodies awaiting burial, wrapped in white plastic bags bound tightly with tan-coloured packaging tape.

About 47,000 evacuees are now huddled in evacuation centres in Washi's wake, mostly in the northern coast of Mindanao, a vast poverty-stricken island troubled for decades by a Muslim separatist insurgency.

Rescue and relief efforts were being spearheaded by government troops normally assigned to fight rebels elsewhere on the island.

The Philippine health department has so far certified 533 deaths from the disaster, said the national disaster council's executive director Benito Ramos.

At least 239 others are missing, the council said in its latest update.

Philippine Red Cross official Gwendolyn Pang said strict guidelines had to be followed in mass burials, including photographing corpses, listing identifying marks and laying them a meter (yard) apart for possible exhumation.

"I'm sure their families will look for them," she told.

President Benigno Aquino is set to visit the disaster zone on Tuesday after ordering a review of the country's disaster defences.

Pope Benedict XVI prayed for the victims of the latest natural disaster to hit the largely Roman Catholic archipelago, which is also prone to earthquakes and volcanic eruptions.

The United States offered assistance as Manila appealed for help to feed, cloth and house the thousands sheltering in evacuation centres, including slum dwellers whose makeshift homes were no match for Washi's fury.

Ramos, the disaster agency chief, said most of the victims were ‘informal settlers’ - a term used for slum squatters who are often unregistered by authorities.

One month's worth of normal rain fell in the affected area within a 24-hour period but residents, who were normally spared from typhoons that regularly hit other regions of the Philippines, ignored warnings to move to safe ground.

Authorities likened tropical storm Washi to Ketsana, one of the country's most devastating storms which dumped huge amounts of rain on Manila and other parts of the country in 2009, killing more than 460 people.