From the official Japanese Immigration site
(link here)ツ
It would appear that there is NOT a policy of granting spouse visas to same-sex partners (whether legally married overseas or not).
However, I find a blog referencing a Yomiuri article from December 29th, 2013 (which is no longer available online) in which it was asserted that the legally married same-sex spouse of an American serviceman was allowed to enter Japan without a visa (waiver?).
I find
an article stating changes in the MOJ policy regarding granting permission for Japanese citizens to marry abroad, but it doesn't seem to directly address whether the policy extended to the granting of dependent visas. (The Immigration site would seem to indicate that it does not).