Japanese have been taught over the centuries that loyalty is the supreme virtue. Loyalty to Japan and to the emperor was inculcated into every child in prewar Japan. The emphasis now seems to be on loyalty to the company employing you, loyalty to your section in the company and loyalty to your immediate colleagues.
Such loyalties are not morally wrong or reprehensible, but under Western ethical codes, loyalty is only one quality that should dictate behavior. Honesty and fair dealing are surely even more important qualities required of anyone in public life or at work. The whistle-blower may be unpopular in his company and with his colleagues, but to punish or ostracise a whistle-blower is to treat honesty as if it were a vice.
Unfortunately it seems clear that in some Japanese companies the exposure of wrongdoing is regarded as an act of disloyalty that must be punished. The tendency in Japan seems to many foreign observers to be to close ranks and do everything possible to cover up wrongdoing or where that is impossible to smooth out the effects of dishonesty and fraud so that the company can quickly get back to "normal." In this case "normal" often seems to mean the continuation of dubious practices.