The Caraga region will continue to experience moderate to occasionally heavy rain on Wednesday, the weather bureau said.
A tail-end of a cold front is affecting the Visayas and the eastern section of Mindanao, the Philippine Atmospheric, Geophysical and Astronomical Services Administration (Pagasa) said.
Residents in Caraga were alerted against flashfloods and landslides.
The Visayas and the rest of Mindanao will have cloudy skies with light to moderate rain and isolated thunderstorms.
The northeast monsoon, meanwhile, continues to affect Northern Luzon.
Cloudy skies with light rain will be experienced over the Cagayan Valley, the Cordilleras and the province of Aurora, Pagasa said.
Metro Manila and the rest of Luzon will have partly cloudy to cloudy skies with isolated light rain. CBB