Flew GA in Japan for a year and had a blast, but it was a long time ago. Aviation laws based on US regs. Work permits were very difficult without sponsorship or marriage (read: you better know someone or have needed skills that can't be obtained in Japan) and have a bucketload of cash and time for the medical and exams.
There aren't a lot of options available for fresh pilots. You have to look to places that have difficulty attracting pilots. Japan isn't one of them. Good luck.