The powerful 7.3 magnitude quake struck the south of the country during the night bringing down buildings and trapping scores of people.
It was much bigger and hit a wider area than the one that struck the city of Kumamoto on Thursday.
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The quake triggered dramatic mud slides which cascaded down on to buildings, ruptured a dam, collapsed bridges and left huge holes in the ground.
Rescue operations at night will be extremely difficult
Many frightened people wrapped in blankets sat outside their homes while others camped out in rice fields in rural areas surrounding the main towns.
Some 422,000 households were left without water and about 100,000 without electricity.
Thousands of troops were sent in to erect tents for evacuees and water trucks were being sent to the area.
Prime Minister Shinzo Abe told a government meeting: “The wind is expected to pick up and rain will likely get heavier. Rescue operations at night will be extremely difficult.
“But there are people waiting for help. Please do your utmost while putting top priority on human lives.”
Parts of the historic Aso shrine, a popular tourist spot that is more than 1,700 years old, has been damaged.
A towering gate, known as the “cherry blossom gate” because of its grandeur when the trees bloom in spring, collapsed.
Eleanor Bley Griffiths, 23, from London, was on holiday with her boyfriend when the quakes struck, in Kyoto for the first one and then Hiroshima for the second.
She said: “We were just in a hotel room... the floor was shaking, we felt a bit unsteady and everything started to rattle.”