In October 2015 I was in Matsue, Japan, and I visited Nakaya Fountain Pen Shop, which is a small shop in a quiet area of Matsue. The shop has been run by the same family since 1918. Unfortunately I didn´t meet the current shop owner, since he was obviously busy in the workshop in the back (I could hear him working, through the open backdoor). I was serviced by a very kind lady, and we managed to understand each other, despite my broken Japanese. I only bought ink, and not pens, since that was not what I was looking for, but I could see they had a fine selection of both foreign and Japanese pens.
Our member VirtuThe3rd has put up some videos of the shop here: