Tokyo / Yokohama / Kanto (or closeish to it)

Please note that none of these options are really in Tokyo / Kanto; they can be potentially done as a day-trip.

Hakushu distillery in Yamanashi is currently accepting tours by online booking @ https://www.suntory.co.jp/factory/hakushu/ (Japanese) or https://www.suntory.com/factory/hakushu/ (English)
Kirin’s Fuji Gotemba distillery in Shizuoka is currently accepting tours by online booking @ https://www.kirin.co.jp/experience/factory/gotemba/ (Japanese) or https://www.kirin.co.jp/experience/factory/english/whisky/ (English)
Newly formed Shizuoka distillery is currently accepting tours by online booking @ https://shizuoka-distillery.jp/tour/
Nikka Miyagikyo distillery is currently accepting guests for tours @ https://distillery.nikka.com/miyagikyo/reservation
Mars Shinshu distillery is currently accepting tours @ https://www.hombo.co.jp/factory/shinshu.html
Asaka distillery in Fukushima is accepting tours, but on a limited basis. Please contact them! https://www.sasanokawa.co.jp/contents/contact.html
Chichibu distillery is not currently offering tours to the public, but if you are an industry professional, please contact them and they may be able to arrange one for you.

Kyoto / Osaka / Kansai

Yamazaki Distillery is currently accepting tours by online booking @ https://www.suntory.co.jp/factory/yamazaki/facility/ (Japanese) or https://www.suntory.com/factory/yamazaki/facility/ (English)
Nagahama distillery in Shiga, producers of the Amahagan brands, are offering tours. See https://www.romanbeer.com/viewing/
Rokkosan distillery in Kobe is accepting reservations @ https://airrsv.net/Rokkosan-Distillery/calendar

Sapporo / Hokkaido

Nikka Yoichi is currently accepting guests for tours @ https://distillery.nikka.com/yoichi/reservation
Akkeshi distillery is not offering tours, but you can check out their virtual tour — https://my.matterport.com/show/?m=mKBGFQy43P1

Helios distillery is NOT currently offering tours, per https://www.helios-syuzo.co.jp/tour

Kanosuke distillery in Kagoshima is offering tours! https://kanosuke.com/visit-us/
Sakurao distillery in Hiroshima is offering tours, but tastings are cancelled. See https://www4.revn.jp/sakuraodistillery/