Hmm, the tuition is extremely low relative to the US. On the order or $4-5k USD/year. I am not sure how many additional fees (like facilities, etc.) there are, but I guess not many. Being self funded was common for Japanese students. AFAIK no international students that I knew were self funded, up to the tail of their graduate program when their MEXT ran out.

Now that I think about it, one thing I am not sure about is if self-funded students' travel/conference fees were covered. I would guess they are covered through a grant and it is just the tuition that is self funded, but I do not know for certain. Going to >1 international conference a year would be far more than the tuition.

So, I would guess it would cost ~10k/year to be fully self funded. You can recoup some of that cost working (on a student visa this is limited though), and your lab may also have an RA stipend (but this is both very low [<$20/hr] and counts towards your 28 hour/week limit).

My advice though is to never do a self-funded PhD. Being a PhD "student" is a misnomer. You are a research employee and should be compensated as such.