Taking a large suitcase onto a bullet train in Japan has always been easy and hassle-free. Nothing needs to be done in advance and there are no fees. However, due to the implementation of increased safety measures for the 2020 Tokyo Olympics, this will all change starting in May 2020.
Next year, when riding the Tokaido Shinkansen, the Sanyo Shinkansen, and the Kyushu Shinkansen, you will need to purchase a reserved-seat ticket and make a reservation for your large suitcase ahead of time. If you fail to make the reservation before boarding the train, you will incur a fee of 1,000 yen (a little over $9).
Large suitcases are classified as luggage with total dimensions (length + width + depth) between 63 and 98 inches (160 and 250 centimeters).
There are currently no plans for any other bullet train lines to implement these regulations before the Olympics next year.