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The village of Kusiong accounted for many of the 50 deaths in the area around Datu Odin Sinsuat town, after heavy overnight rain unleashed floods mixed with mud, rocks and fallen trees that buried the community, the area's civil defence office said in a statement.
Similar avalanches also struck villages in the nearby towns of Datu Blah Sinsuat and Upi, which accounted for 17 more deaths.
Eleven people remain missing and 31 were injured, according to official figures.
Flash floods from rains wrought by Tropical Storm Nalgae swamped nine mostly rural towns around Cotabato, a city of 300,000 people on Mindanao island that was also submerged in widespread flooding.
Many residents were caught by surprise as floodwaters rose rapidly before dawn, Naguib Sinarimbo, the spokesman and civil defence chief for the regional government, told AFP.
Teams in rubber boats had rescued residents from rooftops in some towns, Sinarimbo said.
In recent years, flash floods with mud and debris from largely deforested mountainsides have been among the deadliest hazards posed by typhoons in Philippine communities.
Mindanao is rarely hit by the 20 or so typhoons that strike the Philippines each year and kill hundreds of people. Those that do, however, tend to be deadlier than those that hit the country's main island of Luzon.
A long mountain range walls off most of Luzon from the Pacific, where most storms are spawned, helping to absorb the blow, the state weather service said.
A row of cars sat half-submerged on the street outside, video footage showed.
More than 7,000 people were evacuated from flood- and landslide-prone communities in these areas, the civil defence office said in an updated tally.