Of course when we're talking about Japan, 'ebooks' largely means comics, rather than long-form text.
It looks as if the format situation is just as fractured as it is in the West:
ebookjapan uses a .ebi format while
Papyless uses XMDF, and there seem to be a range of other formats as well like T-Time. Both EBI and XMDF seem to be closed proprietary formats whose main aim is to accommodate DRM.