What, they did not consult the Health Ministry? Or the Army?
Or the Godzilla Watch and Fight Service?
Seriously, either those guys are very naive, or they were hoping to trick the Japanese government into implicitly recognizing Bitcoin as something that it is not -- a currency, financial instrument, securuty, etc..
Whatever bitcoin may become in the future, for the Japanese government (and most other governments, it seems) it is still a fantasy thing, that "exists" only as numbers in some database maintained by a non-official organization: just like videogame points and weapons, or real estate on the moon. In the eyes of the law, MtGOX is just a company that lets customers play with those numbers for a (real) fee.
Therefore, it is no surprise that the institutes that regulate Japan's financial system have refused to intervene. Would they bother with a videogame weapons exchange that refuses to deliver the Elfin Swords and Level 3 Magic Wands that clients have "bought" them with real money?
On the other hand, Japanese common justice
can act on MtGOX, just like it can act on any business that fails to honor the contracts (even if implicit) that it made with its clients, or violates some general commerce law. Common justice can force the company to honor the contracts, or declare bankruptcy if it can't. It does not matter what the company does or trades, as long as the clients can define and prove their losses.
Lawsuits are the standard instruments that customers are expected to use when a company defaults on their contracts. Why are MtGOX clients so reluctant do do the natural thing?