Kagoshima - Amami-Oshima - Tokunoshima - Okinoerabujima - Yoronto - Motobu - Naha
Route	Frequency	Duration	2nd class (without bed)	1st class	Car (4-5 meters)
Kagoshima - Naha	3-4 per week	25 hours	14,000 yen	28,000 yen	101,000 yen
Access to: Naha Port, Kagoshima Port Operated by: A Line

 
Aomori and Hokkaido:

Hachinohe - Tomakomai
Route	Frequency	Duration	2nd class (without bed)	1st class	Car (4-5 meters)
Hachinohe - Tomakomai	4 per day	7-9 hours	4,500 yen	9,000 yen	23,000 yen
Access to: Tomakomai Port Operated by: Silver Ferry

 
Seto Inland Sea (Seto Naikai):

Yawatahama - Beppu
Route	Frequency	Duration	2nd class (without bed)	1st class	Car (4-5 meters)
Yawatahama - Beppu	6 per day	3 hours	3,000 yen	5,500 yen	12,500 yen
Access to: Beppu Port, Yawatahama Port Operated by: Uwajima Unyu Ferry

 
Okinawa and Kagoshima:

 
Access information for selected ports:

Otaru, Hokkaido
Otaru Ferry Terminal is a 10 minute bus ride from Otaru-Chikko Station or a 30 minute bus ride or 10 minute taxi ride from Otaru Station. Otaru is located 30 kilometers east of Sapporo (620 yen, 30-50 minutes by JR train). More details.

Tomakomai, Hokkaido
Tomakomai is located 70 kilometers south of Sapporo (45 minutes, 2800 yen by JR limited express train, 60 minutes, 1400 yen by JR local trains or 90 minutes, 1300 yen by Hokkaido Chuo highway bus). Tomakomai has two ports, Tomakomai East Port (used by Shin Nihonkai ferries) and Tomakomai Port (used by most other ferries). Tomakomai East Port is located 30 kilometers outside of the city (bus connection from Tomakomai Station), while Tomakomai Port is just a short bus ride from the railway station.

Muroran, Hokkaido
Muroran is located 140 kilometers south of Sapporo (135 minutes, 2000 yen by Hokkaido Chuo highway bus or 100 minutes, 4500 yen by JR limited express train). Muroran Port is within walking distance from Muroran Station.

Hakodate, Hokkaido
Higashinihon Ferries and Seikan Ferries have separate ferry terminals in Hakodate, both being located about a 20 minute taxi ride north of the city center. The Higashinihon Ferry terminal can also be reached in a 15 minute walk from JR Nanaehama Station, and the Seikan Ferry terminal in a 25 minute walk from JR Goryokaku Station. More details. Donan Ferry is using the same ferry terminal as Higashinihon Ferry.

Aomori
Aomori Ferry Terminal is about 2 kilometers, a 10 minute taxi ride or a 30 minute walk northwest of Aomori Station.

Oarai, Ibaraki Prefecture
Oarai is located 130 kilometers northeast of Tokyo: 100 minutes, 4300 yen by limited express train (JR Joban Line from Ueno, transfer to Kashimarinkai Railway at Mito Station), 160 minutes, 2500 yen by local trains (same route) or two hours, 2200 yen by Ibaraki Kotsu highway bus (from Tokyo Station). The port is a 4 minute taxi ride from Oarai Station.

Niigata
Niigata is located 330 kilometers north of Tokyo on the Sea of Japan coast (130 minutes, 10000 yen by JR shinkansen from Tokyo Station or five hours, 5300 yen by highway bus from Ikebukuro Station). Niigata Port is a 25 minute bus ride from Niigata Station.

Tsuruga, Fukui Prefecture
Tsuruga is located 90 kilometers north of Kyoto on the Sea of Japan coast (50 minutes, 3300 yen by JR limited express train from Kyoto). The port is a 10 minute bus or taxi ride from Tsuruga Station.

Maizuru, Kyoto Prefecture
Maizuru is located 100 kilometers north of Kyoto on the Sea of Japan coast (100 minutes, 3800 yen by JR limited express train or 140 minutes, 2300 yen by bus from Shijo-Kawaramachi in central Kyoto). The port is a 10 minute taxi ride from Higashi-Maizuru Station.

Tokyo
The Tokyo Ferry Terminal is located on a man made island in Tokyo Bay, not far from Odaiba. The closest railway stations are the Kokusai-Tenjijo-Seimon Station on the Yurikamome elevated train (20 minutes from Shimbashi Station) and Kokusai-Tenjijo Station on the Rinkai/Saikyo Line (30 minutes from Shinjuku Station). More details.

Osaka
Most domestic ferries leave from Osaka Nanko (Osaka South Port). The closest station is Ferry Terminal Station on the Nanko Porttown Liner, which can be reached in 10 minutes from Cosmosquare Station, the terminal station of the Chuo Subway Line. The Hankyu Ferries for Kitakyushu leave from Izumiotsu Port, reached by shuttle bus from Izumiotsu Station on the Nankai Line (20 minutes from Nankai Namba Station).

Kobe
Kobe has several ferry terminals, including the Kobe Port Terminal (used by Jumbo Ferries to Takamatsu and the Ferry Sunflower ferries which depart from Kobe) and the Rokko Island Ferry Terminal (used by Ferry Sunflower to Oita, the Hankyu Ferries to Kitakyushu and the Ferry Sunflower ferries which make a stop over in Kobe). The Kobe Port Terminal can be reached in a short bus ride or 15 minute walk from Sannomiya Station or a short walk from Port Terminal Station on the Port Liner. Rokko Island Ferry Terminal can be reached in a short bus ride or 20 minute walk from Island Kitaguchi Station on the Rokko Liner. More details.

Matsuyama, Ehime Prefecture
Matsuyama's ferry terminal (Matsuyama Sightseeing Port) is located a 3 minute bus ride or 10-15 minute walk from Iyotetsu Takahama Station, the last station on the Takahama Tram Line (20 minutes, 400 yen from Matsuyamashi Station). There are also buses from JR Matsuyama Station to the port (20 minutes, 450 yen).

Yawatahama, Ehime Prefecture
Yawatahama Port is a 5 minute bus or taxi ride from JR Yawatahama Station. Yawatahama Station can be reached from Matsuyama by limited express train (45 minutes, 2700 yen) or by local trains (100-120 minutes, 1240 yen).

Kitakyushu, Fukuoka Prefecture
Kitakyushu is Kyushu's second largest city, located just across the straight from Honshu. Kitakyushu's Kokura Station is a station on the Sanyo Shinkansen. Kitakyushu has two ports, Shinmoji Port, which is used by most ferries and Asano Port, which is used by the ferries from Matsuyama. To reach Shinmoji Port from Kokura Station, take a JR local train to Moji Station. From there, it is a 20 minute taxi ride to the port. Asano Port is a 10 minute walk from Kokura Station.

Beppu, Oita Prefecture
Beppu Port is a 10 minute bus ride from Beppu Station.

Shibushi, Kagoshima Prefecture
Shibushi is located 90 kilometers east of Kagoshima and south of Miyazaki (150 minutes by bus from Kagoshima or 140 minutes, 2100 yen by JR local train from Miyazaki). The port is a short taxi ride from Shibushi Station.

Kagoshima
Kagoshima's Port consists of a main port and a new port. The main port (used by most ferries) can be reached in a 10-15 minute walk from Izurodori tram stop or a 15-20 minute bus ride from Kagoshima Chuo Station. The new port (used by Oshima Transport and Marix Line Ferries to Naha) can be reached in a 10 minute taxi ride from Kagoshima Chuo Station. More details.

Naha, Okinawa Prefecture
Naha has three ports: Naha Port, Naha Tomari Port and Naha New Port. Most long distance ferries use either Naha Port or Naha New Port. More details.