It wasn't as bad as it sounds. While "age of consent" was 13, most prefectures already had laws against sexual acts with anyone under 18. So while a 13 year old could technically consent, it was still illegal. It's like buying illegal drugs. It's still illegal even if everyone involved consented.

Despite that, there was no reason for it to be so low and the laws of prefectures didn't always cover every scenario. There has been a push for a while to get the government to crack down on sexual harassment and assault and it seems like it's starting to happen. Hopefully it catches on in other asian countries with lax laws.