Hundreds of flights to Okinawa and other islands in the area were cancelled, stranding thousands of tourists holidaying in the region's tropical beach resorts.
Typhoon Khanun, described as "very strong" by the Japanese weather agency, brought maximum sustained wind speeds of 180 kilometres (112 miles) an hour.
Okinawa's power company said 220,580 households -- nearly 35 percent of the total in the region -- had no electricity early on Wednesday.
An evacuation warning issued across Okinawa and the southern part of Kagoshima region was in place, urging more than 690,000 residents to move to safety, according to the Fire and Disaster Management Agency.
The agency said a total of 11 people in Okinawa were mildly injured.
A 90-year-old man died after being trapped under a collapsed garage on Tuesday evening, public broadcaster NHK reported, adding that strong winds were probably the cause.
The Japan Meteorological Agency warned of flooding and landslides in some parts of the main island of Okinawa.
The typhoon was about 70 kilometres south of Okinawa's remote Kumejima island at 2300 GMT and was moving west-northwest, according to the JMA.
It was expected to cross to eastern China later in the week.
More than 400 flights were cancelled on Wednesday, according to NHK, affecting more than 65,000 passengers.
On Tuesday, tourists made long queues at the main Naha airport, hoping to get back home.
"We haven't been able to secure a hotel and we don't know when the return flight can be booked," Minako Kawakami told local daily Okinawa Times.
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