The official rule is that you can still travel but have to use a non-reserved seat. Though JR Staff generally will issue new reservations for you if a train is not crowded. There is no penalty for missed trains or for re-booking a ticket.

If you miss your reserved Shinkansen (bullet train) in Japan, your ticket is not entirely lost, but you lose your right to a specific seat. Most standard reserved tickets allow you to board a later train on the same day in the non-reserved (Jiyu-seki) carriages (usually cars 1–3) without paying an extra fee. However, you are not guaranteed a seat and may have to stand if the train is full. For certain discounted tickets, such as "Hayatoku" fares, the rules are stricter; these are often "use it or lose it" and may require you to purchase a completely new limited express ticket if you miss the specific train booked. If you realize you are going to be late before the train departs, you can change your reservation once for free at a ticket office or via the app. If you miss the last train of the day, your ticket expires, and you will typically need to buy a new one for the following morning, as reserved seat benefits do not carry over to the next calendar day.