Do you speak of your own first-hand experience, or you got the impression from some material you read? I don't think they are that different from how Mafia is perceived.
Regarding Whataboutism --- I find the accusation really low-effort. My point has never been "The West has/had organised crime so what's the problem with the East having it?"; rather, I am pointing out how you seem to think "The West is superior just because and the East should appreciate being patronisied by the West", while the West had also experienced many of the issues you described. Of course Japan has its problems, but I'd argue it would be up to the Japanese people to figure out what they are and how to solve them.