That's why the hometown tax exists. Small towns use their residence tax money to raise children then none goes back in when the young adult moves to Tokyo and pays residence tax there instead of in their hometown.
Schools are funded by the national government in Japan. These families are not a net-loss on the community, as the parents pay taxes and children are a driver of economic activity.
TIL. Seems like it's a mix between national and municipal funding, but that doesn't really change the overall calculation, as the parents will have most likely paid it back through their own municipal taxes.
That's why the hometown tax exists. Small towns use their residence tax money to raise children then none goes back in when the young adult moves to Tokyo and pays residence tax there instead of in their hometown.