If both parties agree then divorce is very simple. However, if one party refuses things can be drawn out for years (an old boss of mine came into the office literally singing and dancing after the divorce was finalised).

Bare in mind that Japan has no legal joint custody. Also, culturally it's normal for one parent to have zero contact with children after divorce.

Here is an account of the divorce process［1］. I do not know if all the information is still relevant today.

［1］http://www.debito.org/thedivorce.html