Many of the victims were asleep when it struck Mindanao island, killing many in Iligan City and Cagayan de Oro.
Tens of thousands of people have fled to higher ground, the authorities say.
Many people in Cagayan de Oro were trapped in their homes as floods rose rapidly
Rivers burst their banks after 25mm of rain fell in 24 hours.
Large areas were left without power and some domestic flights were cancelled as winds of up to 90 km/h (55mph) swept across the island.
A landslide killed at least five people in the east of the island, the national disaster agency said.
The Philippines are struck by about 20 major storms every year.
Typhoons Nesat and Nalgae battered the country within days of each other in September, leaving more than 100 people dead
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