Guide and information of Japan travel, with access, transportation from Tokyo to Naoshima.
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TOKYO - NAOSHIMA
This site would like to explain several routes (No1, No2, No3, No4 and No5) between modern architect city of Tokyo and the art island of Naoshima in Kagawa (although, Okayama is rather easy to access).
No1. SHINKANSEN (bullet train, super express)
In Japanese language, it is directly translated as New-Main-Line (Shin-Kan-Sen). There are 9 lines operated by 5 JR companies throughout Japan, and one of which is called Tokaido Shinkansen connecting Tokyo and Shin-Osaka, and called Sanyo Shinkansen connecting Shin-Osaka and Hakata (Fukuoka). Through trains go beyond both lines, actually it is as seen as one consecutive line from Tokyo all the way to Hakata (via Shin-Osaka). Naoshima is nearby Okayama which is between Shin-Osaka and Hiroshima.

Hakata <=> Hiroshima <=> Okayama <=> Shin-Osaka <=> Kyoto <=> Tokyo

Okayama station is the terminal for the bridge line called Seto-Ohashi-Line (gateway for Shikoku island for the 88 pilgrimage).

There are Hikari Shinkansen trains every hour from Tokyo. It takes about 4 hours from Tokyo to Okayama. The port is called Uno (not Ueno), sometime there are direct trains from Okayama, but sometime has to change a train at Chaya-machi.

Okayama => Chaya-machi => Uno
Okayama => Chaya-machi => (through the bridge) => Shikoku island

And here's the ferry information between Uno and Naoshima.
There is also a ferry service between Kobe and Takamatsu via Shodoshima.
More islands hopping? Area "A" on this link has Okayama and Takamatsu, island is called Shodoshima.
No2. NIGHT TRAIN SUNRISE
The JR Pass cannot be used for the sleeper (berth) class, but this night train SUNRISE connects Tokyo and Takamatsu via Okayama has some normal seats (carpet floor) which JR Pass holders can take without surcharge. They should not be called "seats" but anyway, it is worth to check your itinerary so that you can maximize your time in Japan. Good thing about the SUNRISE bound for Tokyo is that you will see beautiful sunrise over Pacific Ocean between Atami and Yokohama.

Takamatsu, (no, Chaya-machi does not stop), Okayama, Atami, Yokohama, Tokyo

And here's the ferry information between Takamatsu and Naoshima (Miyanoura). There are both slow ferry and fast boat.

One thing you should dare not to miss is the park, Ritsurin Koen in Takamatsu, perhaps the most beautiful Japanese garden park in Japan, yes, some even says that the Yugen and Miyabi style is beyond the 3 major famous parks (Kairakuen, Kenrokuen, Korakuen).
No.3 JETSTAR (GK JJP)
Other than JR trains mentioned above, there is the LCC connects directly between Tokyo (Narita) and Takamatsu. Usually JPY4,990 one way can be booked very easily, but watch out for the holiday season, well, still far less expensive than JAL and ANA. Now, new LCC called Spring Airlines (9C) has direct flights between Takamatsu and Shanghai.
No.4 SEISHUN 18 KIPPU
This page may explain a bit further, but simply saying, this ticket is only available during students holiday time (Winter, Spring and Summer). It can be JPY2,370 one way between Tokyo and Takamatsu (more or less 13 hours), as well as Tokyo and Uno (more or less 13 hours).

Example-1

Tokyo 05:20 - 07:27 Numazu 07:31 - 08:29 Shizuoka 08:30 - 09:42 Hamamatsu 09:44 - 11:46 Ogaki 12:12 - 12:46 Maibara 12:50 - 15:16 Himeji 15:34 - 15:53 Aioi 15:56 - 17:02 Okayama 17:15 - 18:12 Uno => Ferry to Naoshima

Example-2


Tokyo 05:20 - 07:27 Numazu 07:31 - 08:29 Shizuoka 08:30 - 09:42 Hamamatsu 09:44 - 11:46 Ogaki 12:12 - 12:46 Maibara 12:50 - 15:16 Himeji 15:34 - 15:53 Aioi 15:56 - 17:02 Okayama 17:12 - 18:05 Takamatsu => Ferry to Naoshima
No.5 Ferry between Tokyo and Tokushima (south of Takamatsu in Shikoku island)
This overnight ferry actually goes beyond Shikoku from/to Kyushu island (Kita-Kyushu).

Kita-Kyushu <= (JPY6,900) => Tokushima <= (JPY9,720) => Tokyo
Kita-Kyushu <= <= <= <= <= <= (JPY14,260) => => => => => => Tokyo

It is JPY1,460 about 2 hours JR local train ride between Tokushima and Takamatsu.
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