A further 14 people were missing after the storm, known locally as Paeng, made landfall on Friday packing winds of 75 kilometers (46 miles) per hour.
A death toll of 72 was originally announced by the National Disaster Risk Reduction and Management Council, before being revised down. The group blamed an “overcount” by local officials for the initial figure, according to state media.
Provinces and cities in the south were hit the hardest by the storm. A “state of calamity” has been declared in the city of Cotabatao on Mindanao island, where some 67,000 residents have been affected by the storm.
Upi, a nearby town with a population of just 60,000, has been inundated, the disaster council reported – with thousands being forced to higher ground.
Overall, authorities said that close to 185,000 people across the country have been affected by the storm, with more than 8,000 people made temporarily homeless.
Photos and videos of search and rescue efforts showed bodies being pulled from the water and thick mud and residents trapped on rooftops.
Storms are expected to hit the capital Manila and nearby provinces over the weekend, state weather officials say, as Nalgae cuts through the main Luzon island and heads to the South China Sea.