Japan’s archipelago encompasses over 6,800 islands, of which approximately 430 are inhabited. Beyond the famous island destinations of Okinawa and Miyajima, dozens of remote island communities — each with distinct character, dialects, fishing traditions, crafts and natural environments — are accessible by ferry and reward the travellers willing to slow down and stay.
The Setouchi Inland Sea
The Seto Inland Sea between Honshu, Shikoku and Kyushu contains hundreds of islands, many of which have been transformed by the Setouchi Triennale contemporary art festival — held every three years (2022, 2025, etc.) — into art-island destinations. Key islands:
Naoshima: The most celebrated art island, hosting the Benesse Art Site with museums designed by Tadao Ando (Chichu Art Museum, Lee Ufan Museum, Benesse House) and an art house project transforming traditional homes in the Honmura district. Ferries from Uno Port (Okayama) take 20 minutes; from Takamatsu, 50 minutes. Bicycle rental at the ferry terminal makes the small island completely navigable.
Teshima: The Teshima Art Museum — a shell-shaped concrete structure by architect Ryue Nishizawa containing a single artwork, a perpetually moving pool of water with no visible source — is one of Japan’s most extraordinary art experiences. Teshima also hosts a rice farming revival by island residents after a toxic waste scandal drove the population to near-zero.
Shodoshima: Japan’s primary olive-growing island, connected by ferry to Takamatsu (60–70 minutes) and Himeji. Beyond its olive parks and souvenir culture, Shodoshima has dramatic gorges (kankake gorge), traditional soy sauce brewing operations and a 24-temple pilgrimage circuit modelled on Shikoku’s famous 88-temple route but completable in two days.
Goto Islands, Nagasaki
The Goto Archipelago off the western coast of Kyushu is known for hidden Christian (kakure Kirishitan) history — communities that maintained secret Christian practice through two centuries of Edo-period prohibition. The islands’ stone churches, built after the Meiji-era lifting of the ban, are designated UNESCO World Heritage Sites as part of the Hidden Christian Sites cluster. The main island Fukue is accessible by jet foil (90 minutes) or ferry (3.5 hours) from Nagasaki. The islands’ coastline, camellia forests and fishing village character make them one of Kyushu’s most distinctive destinations.
Ogasawara Islands, Tokyo
The Ogasawara Islands (Bonin Islands) lie 1,000 kilometres south of Tokyo — a 24-hour ferry journey from Tokyo’s Takeshiba pier. This remoteness has preserved extraordinary biodiversity: Ogasawara has the highest rate of endemic species of any Japanese archipelago, including unique birds, insects and plants found nowhere else. UNESCO World Heritage designation (2011) recognised its ecological significance. The ferry runs approximately fortnightly; visitors typically stay 5–7 days combining the arrival and departure ferry schedules. Scuba diving, whale watching, turtle observation and dolphin swimming are the main activities.
Amami Oshima, Kagoshima
The largest island in the Ryukyu chain before Okinawa, Amami retains a distinct island culture — its own dialect, unique weaving tradition (Oshima tsumugi silk ikat) and UNESCO World Heritage subtropical forest (shared designation with Yakushima, Iriomote and Okinawa). The island is accessible by daily flights from Tokyo (2 hours) and Osaka (1.5 hours) or overnight ferry from Kagoshima (12 hours). The main town of Naze has a small but active arts and music scene; the island’s beaches and mangrove rivers are remarkable.
Ferry Travel Practicalities
Japan’s island ferry network is well-organised but schedules are island-specific — confirm timetables on the ferry operator’s website rather than third-party sources, as schedules change seasonally. Most inter-island ferries take cash only (credit cards accepted on larger routes). Second-class accommodation on overnight ferries is carpet-floored dormitory space with bedding provided — bring earplugs. First-class berths (private or shared 4-person cabins) are bookable on major routes and considerably more comfortable. Bicycles are accepted as cargo on most ferries for a small additional charge.