The province of Nueva Ecija in the north was the most heavily affected, with more than 7,000 people forced to evacuate to higher ground after a dyke broke.
In Kalinga province, also in the north, at least 20 houses were underwater and almost 1,500 people were evacuated, the Office of Civil Defense said.
Flooding was also reported in the provinces of Cagayan, Abra and Aurora, stranding hundreds of commuters.
In the southern city of Davao, flash floods washed out at least two houses, officials said.
Rescuers and emergency medical teams have been dispatched to affected areas while the state public works office was asked to begin clearing operations, they said.