The government weather agency is tracking a low pressure area near Davao del Sur.
The LPA was last tracked 160 kilometers east of Davao City, the Philippine Atmospheric, Geophysical and Astronomical Services Administration said in its afternoon bulletin on Wednesday.
Jori Loiz of Pagasa said the weather disturbance had a small chance of developing into a tropical cyclone.
Light to moderate rains and thunderstorms are expected over Mindanao due to an intertropical convergence zone.
Partly cloudy to cloudy skies with isolated rains or thunderstorms would prevail over Metro Manila and the rest of the country, Pagasa said.
The weather bureau also issued a thunderstorm advisory in Bulacan, Metro Manila and Pampanga at 5:30 p.m. The rains are expected to continue in the next two hours.
The public was advised against heavy rains, strong winds, lightning and possible flashfloods.