Residents in a wide swathe of the tropical prefecture, a popular tourist destination some 1,600 km (1,000 miles) southwest of Tokyo, were advised to evacuate as the storm, with winds exceeding 200 kph (more than 145 mph), slowly moved northwest.
In Okinawa's capital Naha, the airport was closed and all flights - amounting to about 900 - cancelled, TV Asahi said. At least 20,000 people were also affected by evacuation advisories in the city, officials said.
Wind and rain were picking up on Tuesday evening, with the storm expected to escalate by Wednesday.
The storm's path remained unpredictable, with some meteorologists saying it could affect eastern China later this week, while public broadcaster NHK said it could turn east, potentially affecting Japan's main islands.
The storm is hitting during the peak summer tourist season, which this year has seen the number of visitors return to pre-pandemic levels. Okinawa is frequently hit by typhoons, but usually later in the year.
Television footage showed most streets in Naha deserted as rain pounded the pavement. At least 180 mm (7.1 inches) of rain was expected to fall by noon on Wednesday, when the storm was likely to brush closest to the area, NHK public television said.
Okinawa is host to the bulk of U.S. forces in Japan, and Kadena Air Base - one of the largest installations - warned personnel to take all necessary precautions.
Severe weather affected other parts of Japan on Monday, with a thunderstorm pounding Tokyo and surrounding areas, leaving some 15,000 households without power at one point.
(Reporting by Elaine Lies; Editing by Stephen Coates and Miral Fahmy)
