The guidelines were issued to the region's more than 44 million residents by experts, convened by the Cabinet Office.
The panel also called on municipalities and households to maintain emergency supplies like food and water in case the 3,776-meter volcano were to erupt.
Mount Fuji last erupted in 1707.
In the worst-case scenario, a massive eruption of Japan's highest peak could spew 30 centimetres of ash (nearly 12 inches) or more over Tokyo, about 100 kilometres (62 miles) northeast of the volcano, the panel said.
This amount of ashfall could destroy wooden houses, particularly if combined with rain, the report said, urging residents to evacuate in such cases.
Even with less severe ashfall, damage to large buildings is expected, like school gyms that are often used as evacuation centres, the report said.
"The basic rule is to stay inside the ashfall area as much as possible and continue living at places like home," the panel said.
"Evacuation and other actions should be considered in case of danger to life such as severe damage to houses," it added.
The importance of stocking up on emergency supplies was stressed by the panel as ashfall could disrupt deliveries of supplies.
Power outages and disruption to mobile signals are expected, particularly when ashfall mixes with rain, the report said.
The water quality could also worsen, and vehicles would be unable to drive on ash-covered roads, the panel said.
The panel stressed their report did not suggest the timing or the possible scale of the volcano's next eruption or ashfall.
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