The quake struck at 5.45 AM (3.15 AM IST today) around 73 kilometres (45 miles) southeast of the city of Davao at a depth of 56 kilometres, the US Geological Survey said.
The USGS said there was a low likelihood of casualties and damage.
The Hong Kong Observatory measured the tremor at a stronger 6.0.
Mindanao is still clearing up after powerful Typhoon Bopha hit the southern Philippines last week killing at least 548 people, most of them on the island.
The Philippines sits on the Pacific Ring of Fire -- a belt around the Pacific Ocean dotted by active volcanoes and tectonic trenches.