The rain-induced floods and landslides are unlike previous disasters in the Philippines, which are typically triggered by more severe typhoons and tropical storms, of which the archipelago nation usually sees about 20 each year.
The agency also recorded more than 300 flooded areas and 20 rain-induced landslides, which collectively have forced more than 80,000 people to take shelter in evacuation centers. Most of the floods have since subsided.
Local media showed images on Wednesday of people crammed in gymnasiums turned into evacuation centers and residents removing debris and cleaning up homes after days of heavy rains.
The state weather agency said occasional light to moderate rains will continue in central and southern areas until Thursday.