A ticket is a terrible thing to lose, especially if you lose it enroute.
To avoid people claiming they had a ticket when they didn’t, the railways will need to see that you are ticketed at all times — from the moment you buy a ticket, to the moment you leave the station exit gates.
This means that if you lose your ticket whilst enroute, you must buy a new ticket. This new ticket will be calculated from the station you lost your ticket until your exit station. In case of doubt, this will be the station of origin of this train service. You will also need to pay a general handling fee (presently ¥2.—).
If you find your ticket before exiting the train, however, and if you have already paid for the extra ticket onboard, the Chief Conductor will issue you with a travel record which you will use to get your extra ticket refunded. You must request the refund immediately upon arrival. Upon refunding your ticket, you will also need to pay any refund handling fees as applicable.
If you lose your ticket and find it again without informing train crew about your loss, you are not subject to any extra fees.
There is a different procedure to follow if you lose your ticket before travel and have to get a replacement before boarding your train, provided the ticket you lost was a personal ticket registered in your name.