Two people were missing after being swept away by strong currents while crossing swollen rivers in the northern provinces of Abra and Mountain Province, the office said.
More than 83,000 people were affected by the bad weather,including some 4,000 residents forced to flee their homes in Manila.
Government offices, all schools, embassies, courts and the stocke xchange in Manila were closed in Manila as a wide area in the capital was flooded following the torrential rains overnight.