People fled into the streets or hid under tables when the 6.7-magnitude quake struck the Mindanao region on Friday, causing buildings to shake and part of a ceiling inside a shopping mall to collapse.
At least 15 people were injured and more than 800 houses damaged or destroyed, the National Disaster Risk Reduction and Management Council said in its latest update.
The death toll steadily rose over the weekend as searchers found more bodies buried under rubble or soil.
Search operations have largely ended, but the disaster agency said it was still receiving data from some of the dozens of villages affected by the earthquake.
"I'm hoping to God that our death toll won't go up anymore, but we're still waiting for the information coming from the regions," deputy spokesman Mark Timbal told AFP.
The state seismology service said the quake was likely generated by the movement of the earth's crust along the Cotabato trench, a long, narrow depression on the seafloor that forms the boundary of one tectonic plate pushing against another.
Quakes are frequent in the Philippines, which sits along the Pacific "Ring of Fire", an arc of intense seismic as well as volcanic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
Most are too weak to be felt by humans.
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