First of all, I don't think it's fair to say that rapes don't happen that much in Japan because the indications are that they do, it's just that the culture, attitudes and the laws in Japan often do not allow women to speak out about their rapes easily. So such cases are grossly under reported.
The Japanese, or perhaps it's more accurate to say the Japanese law enforcers, remain very feudalistic in their views towards rapes and rape victims, despite the fact that Japan has undergone rapid modernization since the late 70s. Law enforcers and police still look at rape victims as being mostly responsible for their ordeals, that they must have done something wrong to have this violent crime happened to them. This thinking is so strong that many women, once becoming victims, choose to keep quiet instead of reporting it to police (still predominantly males) to avoid being humiliated, and therefore, get "raped" psychologically all over again.
If you read the following article about a Jane, an Australian rape victim in Japan, and you will get some sense of what I'm talking about:
Victims finally learning to speak out against Japan’s outdated rape laws
Also, Japan is both a "shame" culture and a patriarchal society, and women do often blame themselves (or told to blame themselves) for having put themselves in a situation that they become exploited. In a bid not to bring disgrace to their families, they suffer the consequences silently.
Or else women are taught to tolerate and make even lighter of a "lighter offense" such as groping, or even date rapes, by laughing it off. I know there are many such exploits happening in karaoke bars and hotels, where women, usually underlings in a company, get groped or worse by a male boss or co-workers. Some Japanese women friends of mine would tell me, during the three stints of my living in Japan, that so-and-so groped them, yet they just laughed it off, claiming "oh, he's just being a male." Part of this attitude may also have stemmed from the fact that in general, Japanese are non-confrontational, especially women.
Of course some courageous women do report about date rapes, but the success rate of winning such suits is so low (again, women's conducts come into serious scrutinization) that many more women learn to keep quiet.
Perhaps it is also this "what can we do about it?" attitude that has indirectly encouraged some of the so-called 'chikan' or perverts, to go on molesting young women on trains and even view it as a sport. One guy I read in the newspaper (in the late 90s) claimed that he had groped some two, three thousand women on the train and later, went on to write a book about it. He clearly was proud of his wrongdoings. That the book was even allowed to get published goes to show how much the society has indirectly "permitted" such crimes to go on.
Check out the following book and perhaps you'll get a better idea about this phenomenon