The Japan Meteorological Agency said a tsunami of up to one metre (three feet) above normal sea levels may hit eastern Pacific coast regions.
The first waves are forecast to hit northern Hokkaido at around 5:00 am and an hour later in Fukushima prefecture, which was devastated by the 2011 tsunami, Kyodo News agency reported.
The meteorological agency warned people to leave the coast immediately but said it did not expect damage from the waves.
Television footage earlier showed officials in Kochi, southwestern Japan, closing a metal barrier to seal their local breakwater in preparation for possible high waves.
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Large areas of the coastline covered by the alert were also hit by the 2011 quake and tsunami, which killed more than 18,000 people and triggered a nuclear accident at the Fukushima Daiichi power plant.
Tokyo Electric Power, which runs the crippled plant, will suspend part of operations scheduled for early tomorrow near the sea shore at the plant in preparation for any waves, Jiji Press said.