No, the age of consent in Japan is 18 (local law matters, not the national "base" law). Let's stop with the uneducated rumors if you want a real debate.
Male dominated society, yes, and it's way too much. Feminists should try to come here if they want to do meaningful stuff.
But anime is not considered really "normal" by most Japanese people, they know it's crazy, they just kinda accept it.
Looks a lot like a legal construct that can be bent however someone sees fit, provided they have the money.
Also, it sheds some light on another thread we had recently: Japan losing interest in relationships. If things really work like described in that link, then it wouldn't surprise me if teenagers first have no interest in a relationship with another teenager due to potential legal consequences, and later on no interest either, because they've already learned to live without a relationship and not gained any experience in forging a relationship.