652 people were killed and 808 others missing in the flash floods triggered by typhoon Washi in the southern Philippines, The National Red Cross reported.
Rescuers teams are still searching for survivors, as naval vessels are scouring the coast along the island of Mindanao while soldiers searched swollen rivers.
According to officials, many bodies remained unclaimed, suggesting entire families had been swept away.
The flash floods were triggered by tropical storm Washi that coincided with high tides, trapping many in their homes.
The major ports of Cagayan de Oro and Iligan were among the areas worst hit on Friday night.
Almost 35,000 people were still sheltering in evacuation centres on Sunday, the National Disaster Risk Reduction and Management Council said.
Many of the bodies were unclaimed after nearly 24 hours, raising the prospect that entire families had died, Philippines Red Cross Secretary General Gwendolyn Pang said.
“The affected area is so wide and huge and I believe they have not really gone to all areas to do a search,” she said.
“This thing happened so fast, it was very overwhelming.”
The navy joined the search for those who had been swept out to sea. About 60 people were reported to have been plucked from the ocean off El Salvador city, about six miles (10km) north-west of Cagayan de Oro.
Former congressman Ayi Hernandez said he and his family were at home in Cagayan de Oro late on Friday when they heard a loud “swooshing sound”.
He said the water rose to about 11 ft feet (3.3m) in less than an hour, filling his home to the ceiling.
The rescue effort, boosted by some 20,000 soldiers, continued through Saturday night but was being hampered by flooded-out roads and downed power lines, officials said.
National TV showed scenes of devastation, with streets strewn with mud and piles of debris. The remains of houses lay alongside cars that had been picked up by the water and left in culverts and along riverbanks.
US Secretary of State Hillary Clinton sent condolences to the Philippines.
“The US government stands ready to assist Philippine authorities as they respond to this tragedy,” Hilary Clinton said.
Weather experts said Tropical Storm Washi dumped more than a month of average rain in just 12 hours over Mindanao.
Although the Philippines is hit by typhoons or tropical storms every year, Mindanao in the south is usually spared the worst of the damage.
Washi reached the western island of Palawan before dawn on Sunday and is moving west into the South China Sea, government forecasters said.
The storm has maximum winds of 80km/h (50 mph) and is expected to move west, away from the Philippines.