The quake occurred at 23:15 (14:15 GMT) at a depth of 50km (31mi), about 80km off the coast of the Aomori region, the Japan Meteorological Agency said. It prompted tsunami warnings which have now been lifted, while waves of 70cm (27in) were seen.
Some train services have been suspended and thousands of homes have been left without power as a result.
Authorities have also warned that a stronger tremor could occur in the coming days - urging the public to remain on high alert for at least a week, according to local media reports.
EPA A small white car has fallen down a hole that has appeared in the road after an earthquake in Japan. It is snowy and the road has been taped offEPA
A car is stranded on a collapsed road in Tohoku, Northern Japan
Addressing citizens affected by the earthquake, Japanese Prime Minister Sanae Takaichi said: "Reconfirm your daily earthquake preparedness, such as ensuring that you secure furniture, and prepare to evacuate immediately if you feel shaking."
Orders were issued for about 90,000 residents to evacuate, according to Reuters news agency.The Aomori prefectural government said around 2,700 homes have been left without power. East Japan Railway has also suspended some services along the north-eastern coast.
The Japanese government has set up a response office within the prime minister's crisis management centre and convened an emergency team, chief cabinet secretary Minoru Kihara has said.
"We are making every effort to assess the damage and implement emergency disaster response measures, including rescue and relief operations," he added.
Following the tremors, Japanese electric company Tohoku Electric Power said no irregularities were reported at its Higashidori and Onagawa nuclear power plants as a result of the quake, Tohoku Electric Power said.
None were detected either at the disabled Fukushima nuclear power station site, the Japanese authorities told the International Atomic Energy Agency.Fukushima was damaged when a magnitude 9.0 quake struck off the country's eastern coast on 11 March 2011.
That quake, the most powerful ever recorded in Japan, triggered a tsunami which swept over the main island of Honshu, killing more than 18,000 people and wiping entire towns off the map.It sits on the Ring of Fire and, as a result, experiences about 1,500 earthquakes a year.
Earlier this year, Japan's earthquake investigation panel said there was a 60-90% chance that a megaquake would occur in the Nankai Trough within the next 30 years, with worst-case scenarios suggesting it would cause trillions in damage, and potentially kill hundreds of thousands.
Earthquakes along the Nankai Trough - an area of seismic activity which stretches along Japan's Pacific coast - have already been responsible for thousands of deaths.
An earthquake of magnitude 3.8 struck Afghanistan on Tuesday, a statement by the National Center for Seismology (NCS) said.Earlier in the day, another earthquake of magnitude 4.5 occurred at a shallow depth of 10km, making it susceptible to aftershocks.
An earthquake of magnitude 5.4 also struck the Indian Ocean on Tuesday, a statement by the National Center for Seismology (NCS) said.
Shallow earthquakes are generally more dangerous than deep earthquakes. This is because the seismic waves from shallow earthquakes have a shorter distance to travel to the surface, resulting in stronger ground shaking and potentially more damage to structures and greater casualties.
Shallow earthquakes are generally more dangerous than deep earthquakes. This is because the seismic waves from shallow earthquakes have a shorter distance to travel to the surface, resulting in stronger ground shaking and potentially more damage to structures and greater casualties.
Afghanistan has a history of powerful earthquakes, and the Hindu Kush Mountain range is a geologically active area where quakes occur every year, according to the Red Cross.
On November 4, a powerful earthquake rattled northern Afghanistan, killing at least 27 people and injuring 956 more, according to Sharafat Zaman Amar. The tremor also damaged one of the country's most beautiful mosques, CNN reported.
Families were jolted awake in the early hours of Monday when the 6.3-magnitude quake struck near Mazar-i-Sharif, one of the most populated cities in the north of the country, at a shallow depth of 28 kilometres (17.4 miles), the United States Geological Survey said, as per CNN.
Afghanistan sits on numerous fault lines between the Indian and the Eurasian tectonic plates, with a fault line also running directly through Herat. Its location on several active fault lines along the collision zone between the Indian and Eurasian tectonic plates makes it a seismically active region. These plates meet and collide, causing frequent seismic activity.
As per the United Nations Office for the Coordination of Humanitarian Affairs (UNOCHA), Afghanistan remains highly vulnerable to natural disasters, including seasonal flooding, landslides and earthquakes.
These frequent earthquakes in Afghanistan cause damage to vulnerable communities, which are already grappling with decades of conflict and underdevelopment and have left them with little resilience to cope with multiple simultaneous shocks, UNOCHA noted.