[odonata]

As I understand it, you must leave the country as the visa is granted before the date for your visa expires. If you fail to do this then you will get a serious black mark against your visa and passport. This can extend to being refused entry to a chosen country for a period of ten years.

You would do best to talk with your representatives in Japan ie.. your embassy or diplomatic representative.

At the worst case you can fly to Taiwan for the day and renew your basic three months as a tourist.