There are no immediate reports of damage, the Guardian reported.
Officials in the Philippines have warned residents to expect waves above normal tides in the next two hours.
Multiple aftershocks have already struck the area, including a 5.9 and a 6.0 magnitude quake within the last half hour.
This comes after a powerful earthquake struck the central Philippines on October 1.
The shallow quake killed at least 60 people and severely damaged buildings and infrastructure in cities nearby.
More than 150 were believed to have been injured.
The 6.9 magnitude quake struck around 10 pm local time, just west of Palompon and close to the city of Bogo in Cebu province, CNN reported.
The Philippines sits along the Ring of Fire, a 40,000km arc of seismic fault lines encircling the Pacific Ocean.
It is home to over half of the world’s volcanoes and frequently struck by powerful earthquakes.
– Additional reporting RNZ
More to come