In October 2015 I was in Matsue, Japan, and I visited Papylos21, which is a large pen and stationery store at the end of one of the shopping streets, near the river. They had a big selection of pens, inks and stationery, and the staff was very friendly. I only bought ink and stationery, and not pens, since that was not what I was looking for. I could see, however, that they had a wide variety of both foreign and Japanese pens.
I met there with our member VirtuThe3rd, who has put up some videos about the shop here: