The epicentre of the quake, which hit on Tuesday, was situated around 25 km from Tulunam, Cotabato province, the same region that was hit by a 6.4-magnitude tremor around two weeks ago which left seven dead and 200 injured, Efe news reported.
A 66-year-old man in Koronadal in Cotabato province died from head injuries while a 15-year-old boy was buried under debris while moving to a more secure area in Magsaysay in Davao del Sur.
According to the latest report from the country's disaster management authorities, hospitals and clinics in Mindanao recorded a total of 394 people injured, however, most of them were concentrated in Cotabato province.
The tremor, which damaged at least 133 public infrastructure facilities in the area and 90 per cent of houses in Tulunan, affected more than 8,400 people, of whom 3,500 were moved to evacuation centres.
Schools remained closed in the affected region on Wednesday and the national police have deployed reinforcement personnel to attend to the casualties, as many of them were still recovering from the effects of the earthquake two weeks ago.
Although the earthquake did not trigger a tsunami warning, it was followed by around 270 aftershocks, one of them reaching a magnitude of 6.1, according to the Philippine Institute of Volcanology and Seismology (Phivolcs).
The temblor was at a depth of 7 km, and its epicentre was situated around 60 km from Davao, the biggest city in Mindanao and the third biggest in the Philippines, where the intensity of the quake was very strong, Philvocs said.
This year, Philippines has been struck by several high-intensity earthquakes, with the most deadly tremor hitting Pampanga province in April, which killed 16 people and another in Batanes in July, which resulted in nine deaths.
The last major earthquake to hit the country took place in October 2013, when more than 220 people were killed in the central Philippines in a 7.1-magnitude tremor.
In July 1990, more than 220 people died in Luzon island in a temblor measuring 7.8 on the richter scale, which was one of the most powerful one to hit the country.
( With inputs from IANS )