Thousands of troops, police and volunteers have been mobilised to help with rescue and relief efforts.
President Benigno Aquino has visited Nueva Ecija and helped distribute emergency supplies in a shelter for those forced from their homes.
Residents of villages further downstream have been warned not to return to their homes.
"They think it is safe already to go back to their communities but we are preventing them right now," Mr Aquino said.
The national disaster agency says 12 people are confirmed to have been killed by flooding, landslides, or falling objects. Seven people also died when a passenger boat capsized in a different storm further south in the country.