“Saving lives is our priority and we are fighting a battle against time. It is critical that people trapped in homes get rescued immediately,” said Fumio Kishida.
He said there was “large-scale damage” and that it’s especially hard to reach the northern tip of Ishikawa’s Noto peninsula, due to damaged roads.
A thousand soldiers have been deployed to the quake area – on Japan’s west coast – alongside police and firefighters, Mr Kishida added.
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Officials confirmed on Tuesday that 30 people had died just in the city of Wajima, near the epicentre, where smoke and embers were still filling the sky on Tuesday.
Many rail services, ferries and flights into the area have also been suspended.
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Noto airport has shut due to damage to the runway, terminal and access roads, with 500 people stranded inside cars in its car park.
More than 140 tremors have been recorded since the quake first hit, according to Japan’s meteorological agency – which has warned more strong shocks could follow.
On Monday night, around 100,000 people were also evacuated from the quake zone and spent the night in school halls and gyms.
Japanese people are well-drilled on what to do in an earthquake and most of the country’s modern buildings are built with some kind of quake resistance.