Starting May 2020, passengers are required to reserve a seat with oversized baggage area when bringing baggage larger than 160 cm/62 inches onto the Tokaido Shinkansen and all JR Kyushu Shinkansen. This size is roughly the same as oversized baggage on international flights.
This policy is not only for JR Pass holders, but for all passengers. Charges (JPY 1,000) will only be applied if passengers do not reserve a seat with large baggage area prior to their travel. If these seats are needed, please notify the agent at the ticket office that the passenger is traveling with large baggage (2 suitcases per person).
Passengers will be charged JPY 1,000 for their large baggage if they travel in non-reserved seats. Their baggage will then be set in a designated area on the shinkansen. Some Shinkansen may not have large baggage areas, please check on the JR website before travelling.
Please kindly check the below information from JR Central HP.
For JR Kyushu, the rule is the same as JR Central. For your reference, please check the following press release (only Japanese) HERE.