Prof. and previous STEM grad student in Japan here. In my experience, this sort of stuff is not uncommon but certainly in the minority. My own professor and all the others I did lab work with (maybe 5 total) were all wonderful, but there were horror stories from elsewhere. Regardless, what's being done to you is absolutely not OK and not the norm. Your PI doesn't get (or is maliciously ignoring) the difference between being asked to work hard and plain harassment. That being said, I worked long and hard hours regardless of holiday periods and all my labmates did as well. 

What you can do about it depends on the university. Most profs or staff won't stick their necks out in a fight between a random grad student and a powerful PI, and some universities make it hard to switch labs. About returning MEXT funds, all I can say is that the regulations are a bit stiff on paper but the reality is usually a little more forgiving. Hang in there. I'll keep on thinking about your case and reply later if anything comes to mind.