Aftershocks on Wednesday continued to rattle Mindanao island, including one of magnitude 5.3.

The latest count published by the National Emergency and Disaster Risk Reduction Council says 111 people have been injured.

The epicentre, at a depth of 22.4 kilometres, was located in the province of Davao del Sur, about 9 kms 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, 6 km from the epicenter, 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.

Australian Associated Press