But most of the smaller islands are only accessible by air or by ferry. Ferry is the cheaper, and often more pleasant, option. Travel between the southern island of Kyushu and Osaka, which can be done by road or train if you're in a hurry, is better enjoyed as an 11-hour cruise through the Inland Sea National Park. Sado , the biggest of Japan's 'other' islands, can be reached from the mainland in 2 hours by ferry or just one hour by jetfoil. Car Rental Public transport is good in the cities and long distances are best covered by air or train.
Car rental is quite expensive so it is best kept for travel to remote or rural areas.
Combined deals, where the car is picked up at a distant airport or train station, are a good option. Let us know.