I don't know much abut the reefs in Japan, but I am SO jealous!!!
You're going to see some crazy stuff that can't (legally) be exported from Japan. The only advice I can give is to choose your dive company in Japan carefully, just like anywhere else.
Around here it's about $300 for the certification and you have some pool dives, some class time, and then you have to go to open water (a lake) and do the "Completion". When you do the completion you need to own your own mask, snorkel, and fins (about $200-300 for a decent scuba-worthy set). Here the lakes are freakin cold, so you also have to own wet suit gloves and boots (another $100). The rental for the gear for the completion (wet suit hood, 2 pc wet suit, tanks, BCD, weights, etc) is another $200.
I just did the Advanced Open Water a couple weeks ago. The deep dive we went to 86 feet (we're at elevation here, so it's an altitude dive and considered deeper), and it was 13C. Froze me arse off. I saw some big Lake Trout in the night dive too.
