Bicycles are not allowed on Trains or Shinkansen in Japan unless they are but into a bag called Rinko bag. Here are some tips that you should follow if you would like to take your bicycle onto a train or Shinkansen in Japan.
It might take an extra 10 minutes to put your bicycle into a bag when traveling on the train, but at least you will be able to take it with you on your journey especially if you are bike touring using Shinkansen.
Mike