Oh ffs not this again.
Japan is basically comprised of 47 states, each with their own minimum age. There's no federally mandated minimum beyond that of the prefectures.
There is 1, maybe 2, that have an age that low.
However there is a federal law forbidding inappropriate acts...

With children, who are defined in that law as anyone under 18.
Most prefectures have it set to 18.
Any prefecture allowing sex earlier than that only allows it between minors or with those in a relationship recognised/approved by all parents of the couple

You should also note that the prefectures who have age of consent set to less than 18 have it set to 16 if following European laws, or those where it's at 13/14 have it set in law as a reference to tradition where marriages could be arranged by parents at that age.
There...