The Department of Foreign Affairs and Trade has upgraded its travel advice, which also sets an 80-kilometre exclusion zone around the Fukushima Nuclear Power Plant.
The travel advice cites the nuclear threat, as well as ongoing aftershocks and the damage to roads, buildings and communications, as reasons to leave the capital.
"Australians in Tokyo and northern Honshuareas should, unless their presence is essential, leave to Southern Japan or elsewhere," the DFAT travel advice says.
Sixteen Australians remain unaccounted for in the worst-hit areas of Japan.
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