The storm barrelled into Mindanao on Tuesday morning, bringing winds of up to 200 kilometres an hour.
Rescuers say they have recovered dozens of bodies of those killed in flash floods and landslides in the Philippines southern provinces of Compostela Valley and Davao.
Army rescue teams are trying to reach the town of New Bataan, one of the worst hit areas on the island of Mindanao.
The storm triggered a landslide which washed the town away, killing 43 people.
Army officials say they lost a patrol base and a rescue truck in a flash flood.
Major General Ariel Bernardo says the first military responders reached the mountain town of New Bataan late Monday, over 15 hours after Bopha made landfall on the eastern coast of the island.
"We have two companies setting off this morning to help in the search and rescue operations, but our military is also a victim of the storm," he said.
"In one of our headquarters, no bunkers were left standing and all our communication equipment had been destroyed."
The small mountain pass leading to the town had been littered with fallen trees and rocks, virtually cutting it off from road traffic.
"We are hoping to fly our helicopters to conduct reconnaissance and search and recovery," Bernardo added.
Typhoon Bopha brought flash floods and power cuts to much of Mindanao, and rescuers are working to clear the roads of debris.
More than 50,000 people left their homes ahead of the storm and spent the night in emergency shelters.
The Red Cross says aid agencies and the government moved quickly to evacuate people before the storm arrived, a move that undoubtedly saved many lives.
The storm's now weakened as it moves over the western Philippine island of Palawan and the South China Sea.
Typhoon Bopha comes after tropical storm Washi hit Mindanao in December last year, killing more than 1,200 and leaving hundreds of thousands homeless.