I finally received a comment from the Japanese Vexillogical Association post:
Kazutaka Nishiura: IJN flags were adopted by the Imperial ordinance of naval flags (海軍旗章令). But there weren't such flag. I guess the flag was not official flag but just marking flag of the navy. Also a flagstaff of the official Japanese naval flag is usually left side of a flag. But the flag is right side. Therefore I guess the flag is not the official naval flag but the marking flag.
The link he supplied goes to this book titled 海軍制度沿革. 巻7 [The Development of Naval Organizations , Vol. 7], which might be a good resource for the Japanese-speakers:

From page 280, but illustrations start at about 283. After you select the page number to open, use the "next" and "previous" buttons to navigate. next = previous = .