major cities and towns provide some kind of public transport including buses and taxis which implies making your way around in Japan is not a difficulty.
Facts about pretty much all sorts of public transport in Japan for example airlines, airports in Japan, bus routes, driving maps and trains in Japan are published here.
The tables beneath will give you more info on the travel choices to get around Japan: Travel by rail, travel by air, and travel by bus and car.
Airports in Japan
Public Transport in Japan
Japanese Public Transport Questions