The quake struck in waters near the remote Barat Daya islands in Maluku province at 8:52 pm local time, 411 kilometres east of Atambua and 425 kilometres south of Ambon, the USGS said.
It was at a depth of 132 kilometres.
Amin Bin Tongke, chief search and rescue official for Maluku province, told AFP officials had not received any reports of casualties or damage.
"The quake is in a really remote area, near a cluster of small islands away from cities or towns, with a very small population," he said.
Indonesia sits on the Pacific "Ring of Fire" where tectonic plates collide, causing frequent seismic and volcanic activity.