Did some searching before. You'll have to learn Japanese language to survive in Japan as most Japanese do not understand English well. Getting around in Japan would be difficult. One good thing is they provide entrance scholarships. Every phd students in Kyoto/Tokyo varsity are funded.
I did half of my PhD in Japan but with a UK university - I'd reccomend this over going straight to a Japanese uni as you don't need the language requirement and the UK uni can moderate any cultural differences that could impede the progress of the PhD (you'll be surprised at how many problems you can come across!) Expect to work a minimum of 12hrs a day (though you're allowed to take naps between lab sessions and during meetings!) and during weekends. It's a lot of hard work but it's worth it!
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