The 3,776-metre (12,389-foot) Fuji last erupted in 1707 but geologists have included it as one of 47 volcanoes in the Pacific Rim country believed to be at risk of eruption in the coming century.
Some 3,900 residents in 26 cities, towns and villages in three prefectures around the volcano were taking part in the drill, said a disaster management official for the Shizuoka prefectural government.
In the city of Gotemba, about 800 people used their own cars to evacuate along designated routes because public transportation is scarce there, the official, Hayato Mochizuki, told AFP.
Elderly people in need of care were moved by bus. Firefighters, police and troops searched for people who could not evacuate in time, he said.
Eriko Yamatani, the state minister in charge of disaster management, and the governors of the three prefectures took part in a video conference to oversee the operation.
On September 27 Mount Ontake, some 120 kilometres from Fuji, erupted without warning -- killing 56 people and leaving at least seven others missing in Japan's deadliest eruption for almost 90 years.
"But because of the (Ontake) eruption, we are conducting the drill in a serious atmosphere."
The Fuji drill -- whose scale was unprecedented -- was based on the scenario that an eruption occurred at a height of about 2,000 metres at 11 am with ash and smoke soaring 20 kilometres (12.5 miles) and lava flowing from craters.
More than 20 concrete blocks each weighing about two tonnes were to be placed to serve as a dyke and prevent the lava from flowing into a city area, Kyodo news agency said.
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