The Yakuza isn't counted, most of what they do is corruption, blackmail and unofficial / off the books crime. There are a bunch of gangs actively working to take their place as well, none of it is being officially counted:

"The Upstart Gangs Filling the Yakuza Power Vacuum"

https://www.nippon.com/en/features/c04205/

That's exactly what I was wondering. As far as I know, many streets in Japan are still ruled by the Yakuza.