The bigger cities all have western style hotels with western style rooms, bathrooms and often western food.
The bigger and better quality western hotels in Japan will also usually have some staff that speak English and often information on hand in English.
There are often ads on this page for good hotels in Japan and for directories of good hotels in Japan.
If you are going somewhere specific in Japan and would like to know a good hotel in that area, please post the details here and we can give you some names.