If you miss a train you have a reserved seat for, then you are allowed to board the next train and take a non-reserved seat. If the availability allows it, then you may get a new reserved seat.
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Depending on the class of ticket you have, you may or may not be allowed to board the next train with the same ticket. According to railway regulations, once you reserve a seat, you are not permitted to use the same ticket to board the next train.
If you miss your train, then you are allowed to take the next train, but will have to take a non-reserved seat (and risk standing). You can ask JR Staff to rebook, but this will be at their discretion. You can always change seating up to 6 minutes before departure at any ticket desk.
We will refund in full with no fees charged. The train you boarded was delayed by 2 hours or more; or alternatively the train operation was suspended at an intermediate station. ? The train was at least 2 hours late arriving at its destination. We will refund the specified amount for each boarding section reserved.
As per section 28.2 of the National Rail Conditions of Travel, “Where disruption prevents you from completing the journey for which your Ticket is valid and is being used, any Train Company will, where it reasonably can, provide you with alternative means of travel to your destination, or if necessary, provide ...
If your connecting train is with the same carrier as the delayed train you will be able to travel on the next available train to your destination. Speak to the train staff to find out if you can board the next train with your existing ticket as you may need to exchange the ticket for a new one, free of charge.
If a train is cancelled (and that's what's happened here) you're entitled to take the next train that matches any restrictions on your ticket. So if your ticket is routed via a certain place, you must go that way, or if it's only valid on a certain train company, you must use that companies services.
Even the Shinkansen (bullet trains) are equipped with several non-reserved seats cars that you can ride with your JR Pass, without booking ticket. However, it is recommended to book a seat in the Shinkansen when traveling during Japan's national holiday's periods.
Some trains might have a stop as brief as 1 minute, while others might stop 5 to 10 minutes due to waiting for other Shinkansen to pass. Regardless, arriving at the platform about 15 minutes before the departure time provides ample mental and physical preparation.
Advance train tickets aren't flexible, so you must catch the train specified on your ticket. If you catch an earlier train, you may have to pay additional fees, so please check with ticket staff at the station.