Japan has one of the most sophisticated rail networks in the world, and its shinkansen (bullet trains) offer a fast, greener alternative to flying. The cheapest option is to buy a Japan Rail Pass, which come in seven-, 14- and 21-day tickets; these can be bought in advance online or via a travel agent and offer unlimited travel on most JR trains nationwide. There are also a number of regional rail passes that offer unlimited travel in specific areas.
Japan has a wide network of buses (and night buses) that cover more rural destinations than the rail network, though if you’re travelling by road, you might as well drive. Rural areas in Hokkaido, Kyushu, Okinawa and the more remote peninsulas are far easier to explore under your own steam. Hire cars are reasonably priced, though you may require an authorised translation of your driving licence.
Japan stretches for more than 3,000km from tip to tip, so internal flights are often the easiest way to travel between the five main islands. Multiple ferry routes also operate here, with the Kagoshima to Naha (Okinawa) route among the most useful, if time-consuming; it takes around 25 hours to reach the southern islands by boat.
AloJapan.com