That's actually a common misconception. 13 is the age of consent set by the federal law as a base line that prefectures are not allowed to go under. Then each prefecture sets their own age of consent, most of which are currently 18. Similarly to how individual states in the US have their own age of consent. The federal age of consent in Japan is severely outdated because all individual prefectures have a much higher age of consent in their local laws. But if a prefecture decided to lower it to the federal standard, my guess is that the federal age of consent would be raised pretty effing soon. As for now, it's just not necessary.
Okay, rant over, I just roll my eyes every time I see someone spreading that misinformation without even bothering with a simple google search.
Forgive me father, for I have sinned.