For the "why" part see example #1 from the [Digital Museum of Plugs and Sockets][1], and more pictures on other pages.  One common style of outlet in Japan has a separate screw connection for the grounding wire, usually under a plastic flap.

For what to do: this toilet seat should be rewired to a standard three prong plug available at any hardware store (NEMA 5-15P for North America).  Like any bathroom outlet, yours verify yours is three prong and GFCI protected, and test the GFCI using the test button.  After all your hiney is right above water, ground is important (and I say that as a fan of keeping ungrounded K&T where appropriate http://diy.stackexchange.com/a/20279/5960 ).

  [1]: http://www.fam-oud.nl/~plugsocket/Japanese_3hd.html