I don't think anywhere in Japan is actually okay with under 16 currently. It's a bit complicated and stupid, really. Alright so here's how it currently goes as far as I'm aware. You may have heard or read that 13 is the age of consent in Japan. There is actually a law involving that age in that context still in the books. This was a statutory rape sort of deal. Do the horizontal mambo with anyone under 13, you go to jail for a while regardless of what the kid said about it.
However, the child welfare act has an article in it that makes fornication with anyone under the age of 18 illegal now too. So, this means you'd pretty much have to be married to legally have sex with someone between 13 and 18 years old. As for the marriage thing, the legal minimum ages for marriage in Japan are 16 for women, and 18 for men. You can't get married when you're under 20 without the consent of your guardians.
Keep in mind I'm not sure how long it's been this way, and that this story isn't exactly something that just came out. It's not exactly impossible that the article in question from the child welfare act was different or didn't even exist in this form at the time the series was written. In short...
TL;DR: Everything I just said may not have even been relevant to this particular story at all, but should more or less be the current situation (unless you're reading this comment like, years after I wrote it, who knows what could have changed in that time except the fact that I just wasted a lot of time writing all of this and you wasted time reading it).