Typhoon Bopha, the strongest storm to hit the country this year, killed at least 52 people in total after making landfall on the east coast of Mindanao island at dawn, packing winds of 210 kilometres (130 miles) an hour.
A mudslide in a mountainous area near an army patrol base in New Bataan town killed 43 civilians and a soldier, and injured more than two dozen others, local military spokesman Lyndon Paniza told reporters by telephone.
An ABS-CBN television reporter said she counted the bodies laid out in a government building that was converted into a temporary mortuary.
An army truck laden with soldiers and civilians was swept away in a flash flood that hit the town, a local official reported earlier.
The typhoon brought driving rain and strong winds to Mindanao, toppling trees and power lines, causing localised flooding and forcing more than 56,000 to seek refuge in emergency shelters, the civil defence office said.
Winds blew roofs off buildings and residents of coastal and low-lying communities moved into shelters as floods hit, residents and AFP reporters said.
Television footage showed logs being swept down a river, utility workers cutting up fallen trees that were blocking highways, and people lying on mats and cardboard sheets on the concrete floors of gyms turned into shelters.
People living in the path of the storm did what they could to protect their homes and possessions.
"We have taken our pigs and chickens inside our house because their shed might be destroyed," said shopkeeper Marianita Villamor, 46, from the southern farming town of San Fermin.
In Cagayan de Oro city, where giant waves crashed down on the shoreline, mayor Vicente Emano told ABS-CBN that police rounded up all residents in low-lying areas and moved them to government shelters.
In Tagum city, hotel waiter Edgie Atilano, 23, said he and his family hunkered down in their home as Bopha bore down.
"At 3:00 am, we were woken by strong rain and howling winds. Trees and branches started snapping off near the house," said the father-of-two.
"This is my first time to experience a strong typhoon. It was a bit scary."
As well as the 44 killed in New Bataan, officials said there were eight other confirmed deaths, all but one of them occurring on Mindanao, with three of the victims crushed by falling trees.
Four fishermen were also reported missing off Mindanao's east coast, said Freddie Bendulo, planning and development officer of Davao Oriental province.
By early evening the weakened typhoon was streaking across the Sulu Sea, having changed course westward in the afternoon after briefly threatening the central tourist islands of Bohol, Cebu and Negros, the state weather service said.
It was heading toward the north tip of the western island of Palawan and the South China Sea beyond.
A total of 146 flights to and from Mindanao and the central islands had been grounded since Monday night and more than 3,000 ferry passengers were stranded as vessels were ordered to stay in port, according to a civil defence update.
Large parts of Mindanao, which is not normally hit by typhoons, were still without electricity on Tuesday night, it added.
Typhoon Bopha comes after tropical storm Washi hit Mindanao in December last year, killing more than 1,200 and leaving hundreds of thousands homeless.