These are some links that I have found that may be helpful. It appears that a number of prefectures have recently changed their laws to specifically allow tandems.

https://www.japantimes.co.jp/news/20.../#.WkUqBHlG3Z5 indicates that tandem bicycles are allowed in eight prefectures including Nagano, Niigata, Hyogo and Miyazaki.

https://www.warmshowers.org/node/142619 states that tandems are allowed in 10 prefectures:
Hyogo, Ehime, Hiroshima, Miyazaki, Saga, Nagano, Yamagata, Nigata, Gunma and Aichi.

******************************????2****************************************. Google translate shows tandems now allowed in Kyoto Prefecture.

Tandem Touring in Japan | Tokyo By Bike - Cycling News & Information from Japan

https://www3.nhk.or.jp/nhkworld/en/n...two/index.html. Currently, 16 prefectures allow the use of tandem bicycles on public roads.