Found the solution. Just in case someone else having the same issue as me, here was how I got around it:
1. Replace calibre ebook viewer with
Amazon Kindle for PC. Nothing beats the official tools...
2, except Amazon does not allow Japanese ebooks on its own Kindle for PC software. The book you bought wont appear on Kindle PC (in fact you cant even register it with a Japanese Amazon account).
To do it, you have to strip Amazon DRM from your books, then manually put it into PC library directory ('my kindle content' in 'My documents'). Dont download then add books to Calibre to disable DRM,
but download them to kindle first then pull them from kindle to put into Calibre.
3, If you reach here by search engines, I assume you already knew how to get around Amazon Japan geographical restriction using VPN.
If not, heres something to start with.
Thats it, enjoy your Japanese novels on Kindle PC with all their glories. I'm not advocating piracy here, you have to buy the books off Amazon JP store yourself.