I learned of this service and thought it would be a good idea to share the knowledge, since I had no idea how to get fingerprinted in Japan.

I recently found a fingerprinting service located in Shibuya, Tokyo, called Fingerprint Room Japan. In order to get a visa to teach English in China, I needed fingerprints done for an RCMP background check. They were able to take the fingerprints for me and have all the documents required sent to me in Japan.
They also offer RCMP and FBI background check certificates, as well as printing out digital fingerprints on fingerprint forms.

Fingerprint Room Japan
https://www.fingerprintroomjapan.co.jp/

Hope this helps!