Gangsters and organized crime in Japan are basically so integrated with the government they might as well be their own branch. The gangs have their own newspapers, run their own charity and relief operations, etc.
www.nytimes.com
Japanese Gangsters meanwhile work to stay out of the public eye. F'rex their standard form of protection racket, called
sōkaiya, involves harassing corporation boards and using blackmail and intimidation on them rather than going into a dry cleaners and breaking things until the owner pays up.
Japanese gangs involve themselves in the expected drug and human trafficking but take care to victimize foreigners, which with Japan's notorious tendency towards insular Japan-first attitudes towards race, lets them get by without the public getting angry about it.
Provides information to combat human trafficking through prevention, prosecution, and victim protection.
web.archive.org
Ultimately the crime is all there it's just carefully hushed up and not counted. Getting back on topic, the Yakuza also tend to have guns despite the supposed bans, and do a lot of stabbing and bomb killing in their efforts too, which are heavily underreported to keep Japan's crime statistics looking good.
japanjunky.com