More than 600 people are feared dead after tropical storm Washi whipped the southern Philippines, unleashing mammoth floods across vast areas of the country.



Relief workers said that 440 people had died and nearly 200 were missing after the storm wreaked havoc, destroying whole neighbourhoods.



About 20,000 soldiers had been mobilised in a huge rescue and relief operation across the stricken north coast of the island of Mindanao, where the major ports of Cagayan de Oro and Iligan were worst hit.



Cagayan de Oro city reported 215 dead, and nearby Iligan city lost 144 residents, Philippine National Red Cross secretary-general Gwen Pang said.



Iligan mayor Lawrence Cruz described rampaging floodwaters from swollen rivers that swamped up to a quarter of the land area of the city of 100,000.



"It's the worst flood in the history of our city," Cruz told GMA television.



"It happened so fast, at a time when people were fast asleep."



The station showed dramatic pictures of a family escaping out of the window of their home in the town as the floods rose, and rescue workers in orange vests shepherding survivors to safety above chest-deep waters.



President Benigno Aquino expressed concern at the extent of the tragedy and ordered government agencies to map out areas in the country most vulnerable to future flash floods.



"These areas will be at risk every year ... The first [step in] mitigation has to be relocation from these areas," he said in a meeting with senior civil defence officials.



Benito Ramos, the head of the National Disaster Risk Reduction and Management Council, said Mindanao residents were warned about the dangers posed by the storm days earlier but elected not to move to safer areas.



He said Mindanao was rarely visited by storms, even as 20 major storms strike the Philippines annually, with most hitting Luzon, the largest and most populous island in the south-east Asian archipelago.



"We expect huge damage, especially on agriculture," Ramos said.



Marlyn Manos, an Iligan resident, recounted how she and her children watched in terror from their rooftop as the floodwaters swallowed up the neighbourhood.



"All the small houses behind ours were destroyed, and many of my neighbours are missing," she said.



Iligan tourism officer Pat Noel said waters began rising shortly before midnight local time [3am yesterday AEDT] as people slept, sweeping houses made of light materials and their inhabitants along the riverbanks.



"Many of them told me they sought refuge on their rooftops," he said after joining the first wave of rescuers at daybreak.



Two of the three rivers that flow into the port of Iligan had overflowed, he added, and a popular radio commentator was among those killed.



Other affected areas on Mindanao included Bukidnon province, where 47 people died, while nine others people were killed elsewhere on the island, the Red Cross said.



US Secretary of State Hillary Clinton sent condolences to the Philippines.



"On behalf of President [Barack] Obama and the people of the United States, I want to send my deepest condolences for the devastation and loss of life caused by flooding from Tropical Storm Washi," Clinton said.



"The US government stands ready to assist Philippine authorities as they respond to this tragedy."



More than 4000 people in flooded areas had been moved to evacuation centres, the disaster agency in Manila said.



AFP