The earthquake struck from a depth of 151 kilometres and hit northern Halmahera, the largest island in the Maluku archipelago and the largest Indonesian island outside of the five major islands.
According to reports, a slight shake was felt for 30 seconds all the way to the Philippines, some 431 km from the epicentre.
No injuries, deaths, or property damage have been reported.
Another earthquake struck Indonesia approximately 21 minutes later, south of Sumbia. The 3.9-magnitude quake came from a depth of 10 kilometres and is on the other side of the Banda Sea.
A volcanic eruption hit Indonesia earlier in the day in East Java. The eruption of the Semeru volcano displaced thousands of people, injuring 41, and killing one.
A spokesperson for the Disaster Mitigation Agency said that ten people who were trapped following the volcanic eruption have been rescued.
It has not been confirmed that the eruption and earthquake are directly related.
The Maluku islands were long known as the Spice Islands, due to their monopoly on nutmeg, mace, and cloves.
The islands sit on what geophysicists refer to as the Halmahera tectonic microplate.