According to Japan National Tourist Organization many foreign visitors mistakenly believe that it is very expensive in Tokyo but this is not really true. Many visitors know about "100-yen Shops" and enjoy shopping at these and other discount shops, while dining out is also becoming more affordable for them. Some would go to soba (Buckwheat noodles) shops to have tempura (Deep-fried in vegetable oil, fish and vegetables) soba noodles, rather than going to tempura shops only to order tempura. Also, they go in a group to enjoy sharing nabe (pan menu). It seems that they really know how to enjoy their stay in Japan in an affordable way," says Mr. Katsuo Tobita, the owner of Ryoken "Shigetsu" in Asakusa,Tokyo.
Japan abounds in accommodations, both western-style and Japanese. Types of accommodation vary widely in terms of style and price. You can choose to stay in the familiar comforts of a western-style hotel, or enjoy the comfort and personal attention of a traditional Japanese inn. By taking time to search out some of the nation's less-publicized types of lodgings, you're sure to find clean and comfortable places to stay that suit your pocketbook. The accommodation charge is subject to a consumption tax of 5%. First class hotels also impose a 10 to 15% service charge as well. Tipping is not customary except at top luxury ryokan, where a guest will tip a maid when she first serves tea in the room.

If you do travel to Japan just don't stay in Tokyo, do some sightseeing as well, the best way to do this is to buy a JR pass (train pass) that you can purchase if you are there on a sightseeing tour.
According to Kintetsu International,Japan has the world's most convenient and efficient railway network. JR Group railways are proud of their international reputation for frequent service, punctuality, high speed, and safety. Travel by train is also the ideal way to view Japan: you can enjoy a comfortable and carefree ride as beautiful panoramas glide before your window ,mountains, forests, lakes, highlands and the sea! The other way to enjoy Japan is to find someone who speaks English, thanks to the Japan/US student exchange program and companies hiring English speaking employees you can in most cases find someone that can help you find some of the best local places to visit and dine.   More detail...