BUT...
You need to read this.
In most places (the apartments we're renting, shopping centres) there are western style toilets. But in train stations, conbinis (convenience stores) and perhaps in Biwako, this might be something to be prepared for.
Being prepared means having talked to someone of the same sex about using them, and actually using them in a 'safe' environment first. Secondly, you should always have a little packet of tissues with you (sold everywhere in japan - even given away as advertising outside train stations!!).