In view of our objective of being self-sufficient during our travels, we used public transportation extensively in Japan. This included buses, subways, local trains, and long distance trains. In fact, one trip, from Kyoto to Koyasan, involved using six trains, one cable car and one bus.
Japan has an excellent public transportation system, however, it is vast and complex. Also, even though English is now being used efrequently, there are still many situations where Japanese is the only language. So, you need to be vigilant in order to make sure you get where you are planning to go.
Here is what we learned from our experience.
Japan Rail, JR, is the primary provider of rail service, both long and short distances. As long as your travel involves changing from one JR train to another, you can get one ticket to cover the entire journey. You insert in the turnstile to get in and when you get out the ticket is returned if you are connecting to the next train. Otherwise it disappears. You can use the automated machines for buying tickets---they are not as complicated to use as they look. Alternatively, in most stations, there is an office where tickets are sold. The sales agents speak sufficient English and are very helpful. We got full day passes when in Tokyo. They allowed unlimited use of the JR system within the Metro area.
One challenge in using the train system is to make sure you get on the train going in the correct direction. Frequently, they use either of the two tracks on a given platform for trains going in either direction, and the names of the stops are written in Japanese. We had to ask people standing in the line to make double sure we did not make a mistake.
Shinkansen system is integrated with the rest of JR trains, so the tickets will be sold at the same place as for the others. Shinkansen trains are frequent, so there is no need to make advanced reservations. I recommend opting for reserved seats instead of going in unreserved compartments (generally cars 1-3). If the unreserved compartments are full, you can end up making the journey standing up. There is some place for heavy suitcase, behind the first row of seats. Most people do not travel with heavy luggage, so you should be fine in most cases.
The subways are run by separate entities and they operate pretty much the same way as the railroads. Each station has a name and a number. So the chances of making mistakes are limited. One needs to know, however, which direction to go, by learning what are the major stations on the way you want to go. Or asking around, as I suggested above.
In buses, you get in the middle door and get out the front. You pay when you get out, either by cash (the machines accept up to 1000 yen, but not 5000 or10000 yens). Bus system also has day-passes so you don’t have to keep inserting coins all day. One problem we encountered is interpreting very complex bus route maps. We used Google maps, which sometimes gave the bus number to take for a specific pair of origin and destination. However, often that information was in Japanese. Also, sometimes the information given was not correct. One time, I was on Google maps in real time as the bus was making progress along its route because I was not sure if it would swing by our Airbnb. Fortunately, the upcoming bus stations were displayed so I had some early warning.
In spite of clear instructions, we sometimes goofed up. On one occasion we got off at a wrong station. We were supposed to get off at Shin (new) Imamiya station on way to Koyasan, and we got down at Imamiya. No problem, we took the next train and got down at the right one. Osaka has multiple stations with similar names so one needs to be very careful.
One time, Meera forgot to take the ticket after it went through a turnstile while entering a station. That would have caused a problem while getting out. We told a transit official, and he opened the turnstile to pull out her ticket. The machine apparently dumps in a box underneath the tickets that not snatched by the passenger.
Another time, we bought tickets that were 50 yens less than they should have been. The turnstile door would not open on the way out. We forced our way out but were immediately met by a guard who asked us to pay the difference. He had all the information needed to catch us right away.
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