The quake struck deep at some 171 kilometres (106 miles) below the earth's surface in the Banda Sea, the US Geological Survey said.
A tsunami alert was initially triggered by the Indian Ocean Tsunami Warning and Mitigation System (IOTWMS).
However IOTWMS followed up with a second bulletin that said there was "no threat to countries in the Indian Ocean".
The quake's epicentre was located in a sparsely inhabited part of the Banda Sea, 380 kilometres from Ambon, the capital of Maluku province.
Local officials said there were no reports of damage or injury.
"The tremor was felt mildly for two to three seconds by the locals, there was no panic and no tsunami threat," disaster mitigation agency spokesman Sutopo Purwo Nugroho told AFP.
A similar 6.1-magnitude quake hit close to Monday's epicentre on 26 February and caused no damage.
Indonesia sits on the so-called Pacific Ring of Fire, a seismic activity hotspot.
It is frequently hit by quakes, most of them harmless.
However the archipelago remains acutely alert to tremors that might trigger tsunamis.
In 2004 a devastating tsunami caused by a magnitude 9.3 undersea earthquake off the coast of Sumatra killed 220,000 people in countries around the Indian Ocean, including 168,000 in Indonesia.
Image of where the quake struck Source: USGS
