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Typhoon Neoguri was due to pass over Okinawa's main island later on Tuesday, with strong winds and torrential rain, BBC said.
Flights have been cancelled and schools shut. Local television footage showed palm trees being tossed by wind.
Forecasters said the storm could be one of the strongest to hit Japan, generating waves up to 14m (46ft).
"There is a risk of unprecedentedly strong winds and torrential rains. Please refrain from non-essential outdoor activities,'' Japan Meteorological Agency (JMA) spokesman Satoshi Ebihara told a news conference on Monday night.
Local authorities urged some 480,000 residents across Okinawa to stay at home or move to community centres for shelter.
More than 50,000 households were reported to be without power, and one oil refinery has halted operations.
As of 12:00 local time (04:00 GMT), Typhoon Neoguri was reported to be heading north at a speed of 25 kilometres per hour (15 mph), with gusts of up to 252 kilometres per hour (151 mph), Kyodo news agency reported.