If Japanese citizens are exempt from having to obtain a visa, what is the 3000 yen fee for?

Caroline, you misunderstood it. If you stay less than 15 days, you needn't apply one in advance. Of course, you needn't pay anything. However, if you stay more than 15 days, then you should apply one in advance. In this case, you should pay 3000 Yen for a single entry one.