The reason for this is that Japan is (still) a strongly patriarchal society, they view the man as the dominant figure, while the female is considered to be the subject who has to obey the man; husband, father, brother, etc.
All of this is reflected in the division in the workforce. While females can represent 50 percent of all the workforce population, they will rarely climb to the top in terms of managerial positions.
This situation has been improving over the last few decades, however, it still has a long way to go.