This is a real issue... It's a dirty word, but we all use it everyday -- the toilet. I am knowledgable on the men's toilets only, but aside for a few minor details, I imagine they aren't too different from the ladies'. The first time you use a Japanese toilet it feels strange, but you get used to it quickly. But actually a majority of toilets you will use in Japan (except in old buildings and schools) are western style or have the option of a Western style. It is either the squat type or the western type with a lot of buttons that do strange things.
An interesting fact is nearly all toilets made in Japan are from a company called TOTO.
You walk into the toilet and close the door (let's hope there is a door). Then turn facing the flusher or the covering (in photo to the right). Then you squat etc... All your toilet-life you have never had to use your legs, but now you must use your legs not only to support yourself, but to balance yourself in the right position just before releasing the... well you know. And be warned the first time will seem strange to you. Don't worry you will get used to it. After you are finished flushing and doing your proper procedures, stand up SLOWLY. Your legs may be asleep depending on how long you were down.
Use this one just as you would back home, EXCEPT... DON'T TOUCH ANY BUTTONS. If you do you may find an unpleasant surprise coming up from the depths. The toilets are high-tech. They have seat warmers, bottom washers, and a number of other things that are scary for the first time gaijin to be messing with! A friend and I went to a restaurant together a few years ago. He excused himself to the toilet while I ordered. He came back about 10 minutes later with a pale, white face. I said, "Are you ok? What happened?" He said, "Don't ever touch those toilet buttons!" He claims he screamed loudly when a gush of warm water came unexpectedly from below. I didn't hear him, but the restaurant was noisy at the time. Well, that is the bit of toilets in Japan. They really aren't as scary as I make them out to be, really.

source: http://www.thejapanesepage.com