We have a bunch of accessible ones we’ve found compiled on Accessible Japan that we can recommend. (Disclaimer, I run Accessible Japan btw)

The custom tour operators can also do tours with a private van etc

https://www.accessible-japan.com/accessible-tours-japan/

Hi there, I am a manual wheelchair user, and I lived in Taiwan for six months. Overall, my experiences in terms of access were mixed. Sometimes sidewalks are either inaccessible or non-existent, and in these cases, I was often left with no choice but to wheel along the side of the road. It wasn’t too bad, though, and you soon get used to it.…

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