Typhoon Neoguri passed over the islands yesterday bringing torrential rain and winds with gusts of up to 151mph.
Flights and some ferry services were suspended, while most schools were forced to close.
The strong winds uprooted trees and tore wooden buildings from their foundations.
Last night local officials said at least 17 people were injured as a result of the typhoon, and a 62-year-old man had died.
In a separate incident, an 81-year-old fisherman was found dead after going missing from a boat.
About 590,000 residents across Okinawa were advised to stay at home or move to community centres for shelter.
Forecasters last night said the typhoon was now headed out over the East China Sea and was weakening.
This led to Japan’s weather agency lifting some of the storm and high-wave warnings issued for Okinawa, the Kyodo news agency reported.
Japan is relatively well prepared for typhoons, but the torrential rains could cause greater damage if the typhoon moves across the Japanese archipelago as it is expected to tomorrow.
Meteorological agency official Satoshi Ebihara said: “Please refrain from non-essential activities and from approaching hazardous areas. Please show extreme caution.”
There were destructive winds, waves up to 46ft high and storm surges that were set to intensify as the storm passed the main island of Okinawa in the evening and headed north toward Kyushu.
Almost 100,000 homes were believed to be without electricity last night.
Television footage showed a building shattered, damaged shopfronts and trees toppled as winds picked up in the Okinawan capital, Naha.
Forecasts show the storm tracking towards Kyushu and then across Japan’s main island, Honshu.
It is forecast to lose more of its power as it moves over land, but heavy rains could trigger landslides or flooding. Such risks are elevated by the storm’s timing, coming at the tail end of Japan’s summer rainy season.
Authorities in China and Taiwan have also warned ships to stay clear of the storm.
Neoguri is a Korean word meaning “raccoon dog”, a knee-high animal that looks like a cross between a dog and a raccoon, but is a separate species common in East Asia.
Okinawa, Japan’s southern-most prefecture that comprises several islands, is home to major American military bases.
About 26,000 US troops are stationed there under a long-standing security alliance.
Officers had evacuated some aircraft from Kadena Air Base in preparation for Typhoon Neoguri’s arrival.