Rescuers struggled to help survivors and a ravaged city prepared for a mass burial as the death toll from devastating flash floods in the southern Philippines rose past 650 on Sunday.

With hundreds more still listed as missing, tropical storm Washi left Philippine territory after dumping heavy rains that overwhelmed rivers in the port cities of Cagayan de Oro and Iligan on Mindanao island at the weekend.

Iligan, where more than 200 people were killed, was preparing to bury unclaimed bodies in a mass grave as early as Monday because of their advanced state of decomposition.

City health officer Liddy Villarin said body bags will be marked for possible exhumation.

"We will put markings on the cadaver bags which will give the physical features of each body before they put them in the mass grave," she said.

Entire villages were swept away by floodwaters as residents, normally spared from typhoons that ravage other parts of the Philippines every year, slept in the early hours of Saturday despite storm warnings.

The Philippine Red Cross said 652 people had been confirmed dead by its field staff and another 808 were currently listed as missing.

Gwendolyn Pang, the organisation's secretary-general, told AFP that bodies buried in mass graves will have to be properly marked, photographed and mapped for future identification.

The head of the government's disaster response agency, Benito Ramos, earlier said its own count stood at 516 deaths and 274 missing but conceded that the toll was likely to rise.

"I'm out here retrieving bodies that are starting to rise to the surface," Ramos told AFP by mobile phone from a rescue boat off Cagayan de Oro.

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, clothe and house more than 35,000 people in evacuation centres.

Secretary of State Hillary Clinton said in a statement: "The US government stands ready to assist Philippine authorities as they respond to this tragedy."

China was one of the first countries to announce cash donations.

A 20,000-strong military force normally involved in fighting Muslim insurgents in Mindanao was leading rescue and relief operations but the efforts were hampered by masses of mud left behind by floodwaters.

An AFP photographer saw a 30-member military and police rescue team landing Sunday in Bayug, a delta area near Iligan that was formerly home to a fishing community estimated by social welfare officials to have had up to 1,000 residents.

The delta had been swept clean of most structures, leaving those left alive having to rebuild huts with scrap wood.

Military reports from Bayug showed 270 survivors had been accounted for.

In Cagayan de Oro, corpses were piling up unclaimed at mortuaries and overworked staff ran out of embalming fluid, coffins and water to clean them.

One establishment, Somo Funeral Homes, turned away the bodies of two drowned children.

"We are already swamped. We only have four embalmers," its owner Ryan Somo told AFP.

Local authorities opened up fire hydrants and residents quickly formed long lines to get fresh water in the city of half a million people.

The Red Cross listed 346 deaths in Cagayan de Oro and 206 in Iligan.

Smaller tolls were reported in other parts of Mindanao and the central province of Negros Oriental.

Ramos, the disaster agency chief, said most of the victims were "informal settlers" -- a term used for internal migrants who are often unregistered.

"They were not prepared for the typhoon," he said, adding that floods struck "at an unholy hour, 2:00 am, when everybody was asleep."

Ramos speculated that climate change could have been a factor in the unusual trajectory of the storm.

"Northern Mindanao is not a typhoon path," he said by telephone.

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.