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If you want to report the suspected crime to the authorities, but are worried about adverse publicity, there are a few things you can do.
You can meet with your local law-enforcement agency in advance and set up a procedure that allows you to report suspected crimes while minimizing adverse publicity. If you have an existing relationship with the agency, this can be very effective.
More frequently, however, companies are enlisting the assistance of cybercrime and security consultants and keeping them on retainer. They have contacts within most federal and local law-enforcement agencies and can use those contacts to facilitate the investigations and handle the matter in a discreet fashion. The right firm handles things from the time the suspected crime is discovered through the prosecution and is often schooled in public relations, as well.