Zenyoji Temple is a small temple in Tokyo that is home to Yogo no Matsu, Japan’s widest pine tree – and it is incredibly wheelchair accessible.

https://www.accessible-japan.com/places/japan/tokyo/edogawa/attractions/zenyoji-temple/

Thanks to @alison we were able to add Nagoya Castle to the website!

https://www.accessible-japan.com/places/japan/aichi/nagoya/attractions/nagoya-castle/

Literally surrounded by the tall buildings that make up Shinjuku, Hanazono Shrine is a great example of the ancient and modern mixing in Japan. While the main hall is not accessible, the grounds are easy to see for wheelchair users.

https://www.accessible-japan.com/places/japan/tokyo/shinjuku/attractions/hanazono-shrine/