The US Geological Survey said the quake had a depth of 38 kilometres (24 miles) and hit at 02:17 am (1817 GMT Friday) some 87 kilometres east of the city of Butuan.
The USGS had initially reported the quake as having a magnitude of 6.4, but revised it to 6.1.
The Philippine Institute of Volcanology and Seismology measured the quake at 6.5 magnitude and warned that aftershocks were expected.
No damage or injuries were immediately reported, regional civil defence officer Troy Callo told AFP, adding that some local residents complained about “objects falling inside houses”.
The Philippines is one of the most disaster-prone countries in the world, with an average of 20 typhoons battering the island nation every year.
It also sits on the Pacific Ring of Fire—a belt around the Pacific Ocean dotted by active volcanoes and unstable ocean trenches.
A 7.6-magnitude quake hit the country’s east coast on August 31, triggering a tsunami alert that forced more than 130,000 to flee their homes and causing a landslide that killed one person.