Typhoon Bopha has battered southern regions, especially the Compostela Valley in eastern Mindanao, where government information officer Fe Maestre told the BBC that as much as 70% of the area's agriculture has been damaged.
At least 43 people were killed when mud engulfed a school and village hall being used as evacuation centres in Andap village, in the Compostela Valley.
Christian Aid said around 12,000 families had been forced from their homes as a result of the strong winds, heavy rain and flooding. They are now staying in evacuation centres.
Rescue teams are in the affected areas but have faced challenges in reaching isolated communities.
Fallen trees and collapsed bridges have rendered some roads impassable.
Bopha is a stronger storm than Typhoon Washi, which struck one year ago killing 1,300.
After Washi, Christian Aid funded the implementation of text message-based early warning systems.
The systems have proved valuable in helping some communities prepare and coordinate their evacuations this time round.
"Christian Aid and our partners are monitoring the situation carefully and coordinating closely with other organisations in readiness to assess the situation and respond," the aid agency said.