The quake on Monday struck rural Niigata prefecture, about 250km north of Tokyo in the same area where the country's deadliest quake in nine years killed 23 people and injured more than 2000 two days ago, local media reported.
There were no immediate reports of injuries or damage.
More than 240 aftershocks have been felt in the area since Saturday's earthquake which measured 6.8 on the Richter scale.
Niigata was then hit on Sunday afternoon by two strong aftershocks of 4.9 and 4.6 on the Richter scale.
The first quake cut off power to 280,000 households as some 42,000 residents in Niigata were forced to evacuate.
The quakes hit as Japan was still reeling from Wednesday's Typhoon Tokage - a ferocious storm that left 79 people dead.
The Kyodo news agency reported that five of the dead had been buried alive, and that aftershocks had rumbled on for more than 13 hours after the earthquake.