About 20,000 evacuees in the Caraga region returned to their homes as floods subsided, the regional risk management group said.
However, more than 5,000 families are still at evacuation centers in various towns in Agusan del Sur, Agusan del Norte and Dinagat.
Infrastructure damage in Caraga is estimated to cost more than P135 million.
A third casualty was reported in the region, 86-year-old Estrella Perpas, who drowned in Barangay Lemon in Butuan City.
Heavy rains brought about by the tailend of a cold front submerged parts of Caraga on January 11.
On Saturday morning, Sagip Kapamilya distributed food packs to affected residents in Loreto municipality, which was placed under a state of calamity.
The Butuan city government has raised the red flood alert level after the Agusan River reached 3.1 meters above sea level.
Forced evacuation was implemented in coastal areas and low-lying villages.