Urban Transport
Japan's transport system is one of the world's most advanced. Its railroads relate almost all the country parts. City transports are bus and taxi (24/7) while ferries connect Tokyo, Osaka, Kobe with Hokkaido and Kyushu's major ports.
Japan's transport is by no means cheap. But proper planning by hotel discounts, using passes and night buses or ferries can save a lot on inter-city travel.