Typhoon Trami, rated Category 2, is the latest storm to threaten Japan in a year of grim weather-related woes, including punishing heat, heavy rains and landslides.
Outlying islands in the Okinawan chain, around 1,000 km southwest of Tokyo, were being pounded by heavy rain and high tides on Saturday.
Winds with gusts of up to 216 kph knocked down trees, blew off an outer wall from a building and left 17 people injured in Okinawa.
Local officials said no one was feared dead as a result of the storm.
About 195,000 households lost electricity on Okinawa and other neighbouring small islands, according to Okinawa Electric Power.
Public broadcaster NHK said more than 380 flights were cancelled, mainly those flying in and out of Okinawa.
Churning north across Okinawa on Saturday, Trami is then predicted to move across the islands of Kyushu and the main island of Honshu on Sunday, a path similar to that taken by typhoon Jebi early in September.
Jebi, the most powerful storm to hit Japan in 25 years, brought some of the highest tides since a 1961 typhoon and flooded Kansai airport near Osaka, taking it out of service for days.
The season’s 24th typhoon “might cause a catastrophe with storm surges, high waves, powerful winds and torrential rains,” an agency official told a news conference on Friday in Naha, the island’s capital, the local Ryukyu Shimpo newspaper reported.
Rainfall of up to 400mm was forecast for the Amami island region and up to 250mm for Okinawa by noon Sunday, while the storm could generate waves up to 13 metres high around the regions, forecasters said.