Credit card penetration is really low so your other options are bank transfers and CVS (paying at a convenience store). COD is actually quite popular but I can't imagine any SaaS could implement that effectively.

I don't have any experience with direct bank transfer systems in Japan. I believe that a lot of Japanese Banks now offer NetBanking as a payment option for CVS payments but I'm not sure how widespread the use is. I'm also not sure what is culturally common in Japan for billing recurring online services.

Perhaps someone on HN who lives in Japan could comment.

Not sure who you're using as a gateway but I do have memories of being on the line with technical support and a Japanese translator.

Best of luck to you!