Aftershocks continued to rattle Mindanao island, including one of magnitude 5.3.
The latest count published by the National Emergency and Disaster Risk Reduction Council said 111 people were injured, Efe news reported.
The epicentre, at a 22.4-kilometre depth, was located in the province of Davao del Sur, about nine kilometres from the town of Padada, where the municipal market collapsed and caused three deaths.
Authorities have ruled out more victims among the rubble, though it was initially thought there were six others trapped.
In the nearby city of Matanao, six kilometres from the epicentre, a six-year-old girl died when her home collapsed, and an 81-year-old woman suffered a heart attack during the earthquake.
The remaining fatalities were registered in the towns of Magsaysay, Hagonoy and Malita, in the province of South Davao. The missing person is from Sarangani province.
More than 9,700 people were evacuated after Sunday's tremor, which destroyed 74 homes and partially destroyed 125.
In addition, it caused damage to 41 public buildings, 128 schools and 19 health centres.
The Philippine Institute of Volcanology and Seismology has so far registered more than 700 aftershocks, of which about 70 were noticeable.
The tremors have occurred in the same region that in October suffered three strong earthquakes of a magnitude greater than 6 and caused about 30 deaths and injuries to about 600 people.
The last major earthquake to hit the country was a 7.1 tremor that killed more than 220 people in the central Philippines in October 2013. In July 1990, more than 2,400 people died on Luzon island from a magnitude 7.8 tremor, one of the strongest in the country.
The Philippines sits on the so-called Ring of Fire, an area that hit by 90 per cent of the world's seismic and volcanic activity, and is shaken yearly by about 7,000 mostly moderate tremors.
( With inputs from IANS )