Tropical Storm Tembin lashed Mindanao island, home to 20 million people, on Friday with gusts of 125 kilometres (80 miles) an hour and torrential rain, wiping out at least one mountain village and prompting a massive rescue operation over the weekend.
Police said 144 people remained missing while more than 40,000 had fled to evacuation camps as Tembin roared out into the South China Sea early Sunday.
A total of 70,000 have been displaced or affected by the storm according to the International Federation of Red Cross and Red Crescent Societies (IFRC), which warned that continued heavy rain could hamper the search for survivors.
"People left everything behind when they fled for their lives," the IFRC's Philippines operations and programmes manager Patrick Elliott said in a statement.
The horrific tropical storm #Tembin has left 100 people dead and 70,000 displaced. @philredcross is on the ground and providing water, food, and shelter #PressRelease: http://bit.ly/2D4bIBR
The archipelago nation is pummelled by major storms every year, many of them deadly. Mindanao tends to be less affected and officials said this may have caused many to ignore warnings to move to safer ground.
Footage shows vast tracks of land on the island is now under brown water, often waste deep as local try to flee to safer ground.
Local police said 135 people were killed and 72 were missing in the northern section of Mindanao, while 47 were dead and 72 missing in the impoverished Zamboanga peninsula on its western side.
Another 18 people perished in the province of Lanao del Sur in the centre of the island.
One of the places hit hardest by the storm was the mountain village of Dalama, which was virtually wiped off the map as rampaging floodwaters carried away 103 houses.
Footage on ABS-CBN showed houses there destroyed or engulfed by floodwaters and rescuers retrieving the body of a girl buried in a landslide.
Police, soldiers and volunteers used shovels and their bare hands to dig through mud and debris in their search for survivors.
"The flood was already close and the people were not able to get out from their homes," Armando Sangcopan, an elderly male survivor, told the station.
"We called for forced evacuation, preemptive evacuation in certain areas. We are saddened by the (large) numbers of casualties," Romina Marasigan, spokeswoman for the National Disaster Risk Reduction and Management Council told reporters in Manila.
In the town of Kabasalan in Zamboanga, dozens of families huddled in the homes of neighbours on Christmas Eve, two days after floods carried off 40 houses, killing three people with one other missing, said local civil defence chief Junalyn Maravillo.
"This is a disaster. They don't think about Christmas. All they think about is what they will eat for today," she told reporters.
The storm swept into the South China Sea before dawn Sunday after hitting the western tourist island of Palawan overnight Saturday, the state weather service said.
"So far zero casualties, but we have accounts of some people missing," Palawan civil defence chief Zaldy Ablana told DZMM radio on Sunday.
But in a Palawan fishing village, a 53-year-old man was killed by a crocodile while securing his boat in a river.
Tembin struck less than a week after Tropical Storm Kai-Tak left scores dead and more than 20 missing in the central Philippines, straining the disaster-prone nation's already stretched resources.
The deadliest typhoon to hit the country is still Haiyan, which killed thousands and destroyed entire towns in heavily populated areas of the central Philippines in November 2013.