Typhoon Bopha killed 902 people mostly on the southern island of Mindanao, where floods and landslides caused major damage in nearly 2000 villages on December 4, the civil defence office said on Thursday.
A total of 615 people remain missing, it said, a big reduction from the previous tally after rescuers found 296 tuna fishermen who had put to sea before Bopha made landfall.
The typhoon, the deadliest natural disaster to hit the Philippines this year, destroyed 149,000 houses.
About 80,000 people remain in government shelters, where they face months in difficult, crowded conditions as relief officials look for safe areas to build permanent shelters.
The United Nations launched a $US65 million ($A61.86 million) global aid appeal for typhoon victims on Monday, saying more than five million people faced difficult conditions as they seek to rebuild their lives.
The death toll from Bopha could top the 1200 people who died last year when Tropical Storm Washi hit Mindanao's north coast.