The storm is expected to cause the most damage in the northern island of Luzon.
The last review of Nock-ten (named after a bird of Laos) reported 25 deaths, most of them drowned or landslide, said civil protection.
On Tuesday the storm swept the coastal provinces of Albay and Camarines Sur in the south of Luzon, forcing 645,000 people from their flooded homes, said Benito Ramos, head of the National Disaster Management.
“These two provinces are under the water,” he said. “We can not use army trucks as the water level is too high,” he said, adding that authorities were waiting for a lull to send water and relief from the air.
Dozens of flights were canceled because of bad weather, he added.
According to the Philippine weather service the storm is expected before moving to the South China Sea on Thursday.
Philippines, vast archipelago of the Pacific Ocean, are struck each year by a score of typhoons.
Tropical storm and typhoon Ketsana Parma, had caused severe flooding September and October 2009. More than 1,000 people were killed and 10 million affected.