The agency had earlier reported the quake's magnitude at 6.2 before revising it. The quake happened at 6:26 a.m. Jakarta time Thursday (2306 GMT Wednesday), it said.
The epicenter was located 96 km northwest of the provincial capital of Manado at the seabed, with a depth of 300 km, the agency said. The jolts were also felt in the nearby province of North Maluku.
Officials of the agency did not issue a tsunami warning as the tremors would not trigger giant waves.