Another reason it may be in your best interest to stop by a Japanese travel agency before coming to Japan is to check out domestic airfare deals. It’s kind of hard to give specifics here because the airlines often change what they offer, but you should be able to find deals for round trip domestic flights in Japan for around 10,000 yen.
The catch with that, however, is that it will not include hotels. If you are going to need a hotel for your domestic travel, the hotel package deals offered by Japanese travel agencies could be helpful. They often have some really good deals for business travel, couples, and families.
The negative side of travel by air is that it may cost a lot of time and money to get from the airport to where you’re going. I’ve found the Fukuoka Airport and Kobe Airport convenient, but Kansai International Airport in Osaka (the one on a manmade island that needs constant attention) is somewhat removed from Osaka, Kyoto, Kobe, and the rest of the Kinki region it services.
If you know where you’re going to go before you leave your home country you may be able to find deals. Another good option is the Japan Rail Pass I mentioned in a different article on this site.
Japan-Guide writes about some of the details of these special fare domestic air tickets here, but be aware that these rules change quickly and there are blackout dates.
In the end, if you need a hotel and you are travelling within Japan, your best bet may be to go to one of the major travel agencies (JTB and H.I.S. are the biggest… probably best to go to both and compare) and look for a good inclusive package trip that would provide a hotel at a discount.
If you have come with a Japan Rail Pass then you have some more options and can choose the kind of accomodations you want.