Your original post yesterday caused me to realize upon review that I was incorrect in thinking that I had this information...which of course was a major system flaw, since my company markets in Japan.
This information is surprisingly difficult to track down if you don't speak or read Japanese.
The key webpage, I think, is
http://www.pmda.go.jp/english/service/regulations.html. This of course is in Japanese, and machine translations of Japanese are not very good. I'm still unclear on exactly where such reports go, even with the instructions. It seems almost as if paper filings go to the PMDA on behalf of the MOH, but electronic filings go to MHLW.
In any case, I think it's clear that all such filings must be in Japanese only, which means that the filing-preparation individual can sort out the requirements from the provided site.