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Naha is the most common entry point to Okinawa, with flights taking roughly two hours and departing regularly from most major airports in Japan (although no direct flights from Sapporo) and several nearby international hubs (Hong Kong, Taipei, Seoul, Shanghai). Most odysseys through Okinawa begin here before moving farther into the archipelago, but there's no reason not to start farther out and work your way back: flights connect directly to Miyako Airport from Osaka-Itami and Tokyo-Haneda, and to Ishigaki from Osaka-Kansai, Kobe, and Tokyo-Haneda. Flying from Naha to either one takes around an hour. Travel agents anywhere in the country can arrange tickets for you. Booking early can get you a significant discount. It is also worth checking on the prices of flight hotel packages that, if booked more than two weeks in advance, can be cheaper than the flight alone.
Public transportation in Okinawa leaves a lot to be desired. Naha is serviced by a handy monorail running from the airport through the city and terminating at Shuri Castle, taking less than an hour end-to-end with trains running about every 10 minutes. Outside the city things are less promising. The story is the same on each of the islands: yes, buses link to urban centers and popular tourist destinations, but schedules are inconvenient, hard to decipher, and confining. Budget for rental cars to make the most of your time on the larger islands.