Guide and information of Japan travel, with access, transportation from Tokyo to Naha, Ishigaki, Miyako, Hateruma, Yonaguni.
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This site would like to explain several routes (No1, No2, No3, No4 and No5) between Tokyo and the south tropical island. No5 is Taiwan route as well.
No1. Easy Comfortable Flight (ANA or JAL) and LCC (Low Cost Carrier)
There are everyday 50 - 60 flights up and down between the capical city and the southern used-to-be kingdom island. Both major companies and SKY have both Haneda route and Narita route, but Haneda Airport has more flights compare to Narita Airport.

Fare varies from JPY6,790 to JPY48,390 (Premium Class) one way. The cheapest must be booked 2 -3 months in advance, and it tends to be sold out within 10 minutes from 09:30AM Japan Standard Time each day (for example, buy ticket on August 20th for fly on October 20th). No one pays for the normal fare except government related business trip, but now wise traveller would pay half of the tariff with stock benefit which you may be able to purchase at discount ticket shop in Kanda, Ueno, Asakusa and Shimbashi. It is worth to get the normal fare ticket with stock benefit (50 percent discount) so that your travel can be very flexible (refundable, reroutable, change-reservation-possible, no limitation, no stress).

If you were connecting to remote islands from the main island (Naha, Okinawa), for example, Yonaguni, Ishigaki, Miyako, both ANA and JAL has connecting-discount-rule as well. You may get special discount (Star Alliance and One World) for those tickets flying all over Japan, too (only about JPY10,000 for any one segment despite distance, from point A to point B as long as there is a direct flight). Now ANA has Sapporo (CTS) - Okinawa (OKA) one shot flight (the longest distance within Japan, 1397 miles) as well as Tokyo (Haneda) - Ishigaki island (ISG) which is 1228 miles.
No2. Bus (Nishitetsu Bus (semi compartment seat), JR Bus Kanto, Willer Express, Nishi Nihon JR Bus, JR Kyushu Bus) and ferry
Mostlikely, you may be interested in stopping over Takayama, Nagano, Kanazawa, Kyoto, Nara, Kobe, Kurashiki, Hiroshima, Nagasaki, Beppu, Kumamoto and more!? Without JR Pass, slow bus ride would give you many chances to view Japan sceneries along the way. As slow you go, more you can see, in which way, bus is recommended. Love slow but easy also required? The minimum transfer to the southern ferry port Kagoshima from Tokyo, the shortest route would be Tokyo => Hakata => Kagoshima, yes, just two buses with one transfer. From Kagoshima, there is slow ferry with stopping Kikaijima, AmamiOshima, Tokunoshima, Okinoerabujima, Yorontou and Motobu as well as direct ferry to Naha, Okinawa.
No.3. FERRY (A"Line Tokyo on Ro-Ro, A"Line Osaka/Kobe, A"Line Kagoshima, Marix Line
Mostlikely? you may get bored while you are slowly travelling to the west and to the south by bus or by train. How about being part of Pacific Ocean? Not only from Tokyo port, but there are also ferry service from Kansai Area (Osaka and Kobe) and the southern most of Kyushu (Kagoshima). Advantage is to float on the sea all the way, benefit is that you can think about your life, or that you don't need to think NOTHING (for 72 hours from Tokyo to Okinawa). Japan is consisted of some 3000 islands on the north-eastern-edge of Asia. Without ferry ride, you would not cover the country.
No.4 SEISHUN 18 KIPPU (the most cheapest way from Tokyo to Kagoshima, only JPY4,740) or JR Pass plus ferry
It takes two full days for Seishun-18-kippu (or 8 hours Shinkansen rides) plus ferry, which means that it may cost you one night extra at accommodation. Truly lowest cost with consider of accommodation and three-meals would be, as mentioned above at No.1, Vanilla Air or JetStar Japan for JPY6,000-ish one way from Narita direct to Okinawa (OKA). More detail can be found at this page. For rail fan, following time scheduler is useful.

HyperDia : Digital time table, route and fare search
Japan Transit Planner : Route found?
No.5 Hopping islands flights
Following airlines have the island hopper routes along the archipelago of Japan, Taiwan, Philippine, Malaysia and Indonesia.

EVA AIR : Star Alliance
CHINA AIRLINES (not Air China) : Sky Team
PEACH : Japanese LCC
Scoot : Singaporean LCC
Vanilla Air : Japanese LCC
JetStar Japan : Australian/Japanese LCC
Where is Asakusa
LCC (Low Cost Carrier)
Japan Rail Pass
Rail Passes
Special Train Tickets
Narita Airport
Haneda Airport
Japan in Asia
From/To elsewhere
Tokyo - Kyoto
Tokyo - Takayama
Tokyo - Naoshima
Tokyo - KumanoKodo
Tokyo - Sapporo
Tokyo - Okinawa
Area by Area
Chubu Hokuriku
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Kyushu Okinawa
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