An earthquake measuring 6.1 magnitude has struck eastern Japan, the US Geological Survey said.
There was no immediate tsunami warning, or reports of damage or casualties.
It is the third quake to hit the country in less than a week.
Nearly 50 people died when a series of quakes struck late last week.
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More than 200,000 people have been told to evacuate their homes in the wake of a powerful earthquake that hit Japan leaving as many as 40 people dead.
Japanese authorities have issued evacuation orders to around 240,000 people amid growing fears of landslides and overcrowding at emergency shelters set up to house those affected by the 7.3 magnitude tremor.
Rescue operations launched following Saturday morning's quake are continuing in a desperate bid to find survivors in the rubble caused by the tremor but Prime Minister Shinzo Abe has warned a government meeting that as bad weather continues efforts may be hampered.
He said: "The wind is expected to pick up and rain will likely get heavier. Rescue operations at night will be extremely difficult ... It's a race against time."
An earthquake in Japan has left people in the vicinity in a "state of shock".
Joseph Fowler, who lives in Kumamoto city near to where the 7.3-magnitude quake hit, says the area is better known for volcanic activity.
Mr Fowler's apartment, which he shares with his wife, was left in disarray, something he described as a "terrifying" experience.
He compared Saturday's earthquake in southern Japan to a "war zone", and said people were scared a bigger quake could hit at any time.
At least 25 people are feared dead so far and many hundreds injured.
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A small eruption occurred at a volcano in southern Japan following a magnitude 7.3 earthquake.
The Japanese Meteorological Agency has kept its alert level at 2 on a scale of 5 for Mt. Aso.
The quake, the second in as many days in the region, has killed at least 15 people and left hundreds injured.
The natural disaster has also hit economic activity in the southern island of Kyushu.
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A 7.4-magnitude earthquake has struck near Kumamoto in southern Japan.
Japanese broadcaster NHK said a number of calls were coming in from residents reporting people being trapped inside houses and buildings.
The quake hit at a depth of 40km (25 miles). The scientific agency earlier reported a 7.1 quake with a depth of 7km near the same location.
The Japan Meteorological Agency issued a tsunami advisory, urging people to leave coastal regions but it was lifted 50 minutes earlier.
There are fears that some people may be trapped in collapsed buildings and rescue services are working through the night.
A powerful earthquake has hit southern Japan, leaving nine people dead and more than 750 injured.Read the full story ›