Sunday's tremor cracked schools, toppled homes and injured dozens but largely spared big cities on the island of Mindanao, which is still recovering from a string of deadly quakes in October.
Searchers pulled the bodies of two victims from a collapsed market building in the town of Padada as they hunted for possible survivors trapped under the debris.
A young child was also killed in a neighbouring town when the family home collapsed.
"We could not yet determine ... exactly how many are still trapped," fire official Fred Trajeras told reporters, referring to the market building.
"Our priority is (finding) signs of life, which we hope we can still rescue," he added.
The collapsed building was near the epicentre of the 6.8 magnitude quake and is in the same region that was hit by three tremors above 6.0 in a matter of weeks in October.
Those quakes killed some two dozen people and forced tens of thousands into shelters as well as heavily damaging homes and offices.
The Philippines is situated on the Pacific "Ring of Fire", an arc of intense seismic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
Searchers were fanning out across the quake hit areas of Mindanao on to fully assess the damage, but have already reported several schools and hospitals were cracked.
President Rodrigo Duterte, who is from Davao and was there during the quake, was not hurt.
"The first lady... said the car she was riding (in) was swaying," spokesman Salvador Panelo said.