Japan's transport system is very well done up. However, train travel is the most convenient form of transport. Getting access to a Japan Rail Pass is a good idea because it offers you unlimited travel across the Japan Railway. Other transport options include taxi, plane, bus and car.
Flying is not really necessary in Japan. It's more of a luxury. Flying is a good option to get to the remote islands such as Okinawa, Kyushu and Hokkaido. Narita Airport sees a lot of domestic flights coming and going. Kansai International Airport also has some domestic flights.
Japan's railway system is very efficient, covering nearly the entire country. Shinkansen trains are very popular and have a good frequency. Ordinary trains include regular trains, express trains, liner trains and limited express. Smoking is not allowed aboard any of these trains.
You can get around by car, bus and taxi here. The buses include local buses and highway buses. Japan Buss Passes also exist, valid for 2 months. Taxis are available everywhere, but are actually quite expensive. Apart from that, you can also rent a car. These services are also available online, for booking. Bike rentals are also available.