Here is a list of ferries I have used. The sites are all in Japanese so you need to use Google Chrome and have it set to auto translate Japanese to English (or your language). It will not be perfect but enough to figure out the times and price. Some of the prices I have paid on ferries show on my best Japan motorcycle roads map and I may expand this later but prices will always go up slightly so best look on the operator sites.
A few tips when reading the sites. Motorcycles are different to cars and will often be listed with bicycles or as special baggage. Some ferries will have a scale of pricing for motorcycles based on engine capacity. Antiquated thinking now days when a large capacity sports bike will weigh less then a old smaller machine but don’t concern yourself. The pricing for two wheelers on most ferries is not expensive. Be aware also that different timetables may operate in holiday season or low season so look carefully at the info and see if there is a 2nd timetable listed as well. Look at the menu titled Access to see where the ticket office is or confirm you have right dock in your GPS.With a couple of exceptions you cannot make any reservation for motorcycles. (but need to for cars) Going to or from Hokkaido always needs a reservation.
To use a car ferry in Japan follow theses steps. Always have enough cash, some will take credit cards but many won’t. Arrive well in advance, motorcycles board first and boarding can already be underway 30 minutes before departure on big ships. First look for the ticket office and have your motorcycle paperwork with you. Some operators require you to fill out a form for a ticket, this will be all in Japanese. Make sure you have Google translate on your phone and use the camera photo translate function to try work it out. From, To, Name, Bike engine size, number plate is usually all that is needed. If really confused try some then go to counter. Always have MapsMe or other offline map program on your phone with destination port pinned so you can point to where you want to go. A motorcycle in Japanese is Otobai pronounced like this ‘Oh-Toe-Bye’. It can help to show your bike paperwork and have a photo of it that shows the model number Z1000, FJR1300 etc.
At the ticket office there is usually a photo diagram or map of where the loading point is, take a moment to study that. If you are given a luggage label this needs to be tied to your mirror as this tells the staff which port you will depart on a multi stop sailing and they will place you at right spot in the boat, facing right way for that stop. You can leave everything on the bike, Japan is super safe honest place nothing will be touched. Make your way upstairs to the passenger area which is likely to be carpeted floor with pillows where people will be lying down taking a rest. Remove your boots before going on that area. There will be vending machines for cup noodles and hot or cold drinks on larger ships, clean toilets and possibly some pachinko/slot machines.
Just one route I know of has a kiosk and that is from Wakayama where you can get a breakfast obento. Take a nap then when close to the port announcements will be made and music played and everyone goes down into the hold. Motorcycles have to wait as they are parked in by cars so take your time putting gear on then when signalled start up and depart. On one sailing I was asked for ticket stub when exiting (Tsushima from memory) otherwise you will just ride straight out of the port.
Here is some of the ferry routes a rider might use touring Japan.
Hokkaido ferries (Aomori or Oma)
Mutsu bay ferry (Imabetsu)
Ise Bay ferry (Toba)
Shikoku to Kyushu Ferries
Nejime – Yamagawa ferry (very small arrive early)
Ariake ferry (Nagusu)
There are dozens of small island hopping ferries that operate in the Japan inland sea. I will expand on that more when time permits.
Long distance ferries
Kobe/Osaka to Kyushu
There are other long distance ferries but perhaps rarely used by riders.
Sorry the formatting is messed up, this happen with the blog relocation to WordPress