Forty-nine people were killed in the mudslide- and flood-hit southern mountain town of New Bataan while 51 others are dead on Mindanao island's east coast, regional military spokesman lieutenant colonel Lyndon Paniza said.

The dead in New Bataan included a soldier taking part in rescue operations after Bopha ravaged the island on Tuesday, he told reporters.

Six other army men from the same unit are missing and three were injured, he told reporters.

Twelve others were killed in other parts of Mindanao, while three deaths were recorded across the central Visayas region, civil defence office personnel told AFP.

Officials earlier said they feared the toll would rise further in the day as rescuers begin reaching isolated areas where dozens were reported to be missing.