Most deaths occurred in and around metropolitan Manila, which already was soaked by heavy monsoon rains ahead of Typhoon Nesat's arrival with more downpours and wind gusts of up to 150kmh.
The typhoon blew out of the Philippines on Wednesday and is expected to make landfall on China's Hainan Island on Thursday evening or early Friday.
The Philippine disaster agency says 35 people are still unaccounted for in the floods, and that 108 have been rescued.