It was first registered as magnitude 6.1 by the USGS but this was later downgraded.
The quake was centered around 60 miles south east of Sendai, Honshu, near where a devastating quake and tsunami struck in March 2011.
There have been no tsunami warnings issued, or immediate reports of damage or casualties.
The country is still reeling from a series of strong quakes which struck in the south late last week, killing 48 people.
Powerful aftershocks have continued to keep the population on edge but most have been restricted to the southern Kyushu island.
Hundreds of people in the previously afflicted Kumamoto area of south western Japan have been sleeping in their cars, afraid to return to damaged houses.
Around 100,000 have been displaced and sleeping in evacuation centres.
"I keep thinking the earthquakes will stop, but they just go on and on," one woman at an evacuation centre in Mashiki, one of the worst-hit areas, told Japanese broadcaster NHK. "It's really scary."
Of more than 680 aftershocks hitting Kyushu island since April 14, more than 89 have registered at magnitude 4 or more on Japan's intensity scale, strong enough to shake buildings.
Heavy rain is expected over the area, raising fears that slopes weakened by the quakes could collapse.
Authorities have begun condemning buildings and other structures deemed unsafe. Hundreds of buildings have collapsed, many brought down by their heavy traditional tile roofs.
Though public buildings must abide by stringent safety standards, the law is lax for private homes.
"When a big earthquake hits, structures may sustain damage that's impossible to fix if there's another quake within days," said Akira Wada, professor emeritus at Tokyo Institute of Technology.
Most of those who were killed had returned to their homes after the first quake.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies