The Japanese favorite transportation is the JR, the Japanese Rail. Most people travel on foot though. Japan has 1,152,207 km of highway. Also there are 173 airports and 16 heliports in Japan. There are 1,770 waterways and 630 ships protect Japan's transportation. The types of ships used to protect Japan include 137 bulk, 51 cargo, 15 chemical, 22-combination bulk, 3 ore/oil, 22 liquefied gas, 9 passenger/cargo, and 49 passenger ships.
Most international students will be astonished by the well-developed Japanese transportation systems. "JR" (which stands for Japan Railway) train networks spread throughout Japan. Also, private lines (trains and railways operated by private companies) develop mainly in urban areas. From railroad terminals or major stations, bus routes spread like a finely woven web. Not only Tokyo, but also big cities like Osaka, Nagoya, and Fukuoka have well-developed subway systems. Due to these greatly advanced transportation systems, you will not feel any inconvenience when you go to and from school and work, or travel on holidays. However, most of the fares tend to be more expensive than those in other countries, which may be a problem for you. For more info visit this website: http://www.cia.gov/cia/publications/factbook/