Dry runs of evacuations, rescue operations and fire fighting were carried out across the nation to simulate an emergency response to an imaginary quake with a magnitude of 7.3 hitting Tokyo in the early morning.
"I order all the ministers to do their best to respond swiftly and appropriately by placing top priority on people's lives," Prime Minister Shinzo Abe said.
The nationwide drill is held annually on September 1, known in Japan as Disaster Prevention Day which comes on the anniversary of the 1923 Great Kanto Earthquake which killed more than 100,000 people and levelled Tokyo.
Recent deadly landslides in the western city of Hiroshima have also highlighted the need to guard against a potentially crippling natural disaster.
The death toll has now reached 72 with two others still missing after the massive landslides, triggered by heavy rain, engulfed part of the city in late August.
Last week, the industry ministry launched a public awareness campaign to call on people to stockpile toilet paper, learning lessons from the 2011 disaster during which the country suffered a shortage of toilet roll among other items.
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