PAGASA has placed Siquijor and Bohol under red rainfall warning on Thursday morning.
This means that heavy rains brought by the tail-end of a cold front may result in serious floodings in these provinces.
Even areas that are not prone to flooding may also be submerged.
The weather bureau has also placed several provinces under orange warning.
These are Agusan del Norte, Davao del Sur, Sultan Kudarat, Bukidnon, Dinagat Island, Siargao Island, Surigao del Norte and Surigao del Sur.
Orange rainfall warning means flooding threatens low-lying areas and river banks.
Landslides may occur in mountainous areas.
Meanwhile, yellow rainfall warning has been raised in Agusan del Sur, Misamis Oriental, Camiguin, Misamis Occidental, Lanao del Norte, South Cotabato, Maguindanao, Zamboanga Peninsula, Basilan, Lanao del Sur and Cotabato City.
Yellow rainfall warning means flooding is possible in low lying areas and in communities near river channels and landslides may occur in the mountains.
Heavy rains have been pouring in several areas in Central Visayas and Northern Mindanao since Wednesday night.
PAGASA cites the tail-end of a cold front as the reason.
It has not spotted any low pressure area or storm so far.