Disaster response officials said five people were believed to be trapped in the rubble of the Southern Trade Shopping Centre in Padada, a town on the island of Mindanao located about 20 kms (12 miles) from the epicentre of Sunday's quake.
Rescuers were using chainsaws and thermal imaging equipment to look for survivors, but said there was little hope of finding anyone alive.
"It's very distressing. There's a very slim chance of finding survivors," regional disaster official Christopher Tan told CNN Philippines.
A six-year-old girl was killed when the wall of her house collapsed on her during the 6.8 magnitude quake, the fifth to hit the region since October. Rescuers also recovered the bodies of two women during a night disrupted by several aftershocks.
A further 31 people were injured, said Francis Irag, regional information officer.
Television footage early on Monday showed fire and rescue personnel using torches to search the outside of the shopping centre, a small two-storey building, in darkness. Roads were blocked by rubble and mangled metal.
There were widespread power outages and minor damage to more than 300 homes and eight government buildings, according to the disaster agency's report late on Sunday.
The Philippines sits on the geologically active Pacific "Ring of Fire" and experiences frequent tremors.
