In Japan there are several ‘Cycle Trains’ which allow bikes to be transported as they are without dismantling. Some of these operate all the time while others run during limited periods only such as weekends or when special events are planned. Many are offered by smaller private rail companies in non-urban areas but some major private and JR lines also operate such trains. Some charge extra for bikes and others allow bikes to be transported free of charge. You may have to book in advance to use these trains.
In Japan, traveling on the train with a bicycle is permitted, even on Shinkansen with no extra charge. You can take a bike on any train at any time for free of charge if you store it in a bike bag called ‘Rinko bag’ 輪行バッグ.