The quake struck at 7:58 pm (1158 GMT) Sunday with its epicentre 251 kilometers (155 miles) beneath the Flores Sea, some 93 kilometers northwest of the town of Larantuka on Flores, the Jakarta-based office said.
Police in Larantuka said they had received no reports of damage or deaths.
The US Geological Survey recorded the tremor, which occurred about 1,770 kilometers east of the capital Jakarta, at 6.2 on the Richter scale.
Indonesia sits on the so-called Pacific Rim of Fire, where the meeting of continental plates causes high volcanic and seismic activity.