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.
I found the term "age of consent" confusing. As I understand it, after googling ( I hope I'm not on a watch list now ) is that age of consent means consent with an adult?? Kids who are 12 can consent to having sexual activity with someone 2 years older in canada. No one under 12 can consent to anything ever. So what does age of consent mean exactly? Someone who is 19 years of age an older? What age is defined as an adult? It's different per country right?
Unqualified, it means anyone at least that age. Some jurisdictions have a "Romeo and Juliet" provision that allows anyone under the general age to have sex with someone around the same age, or other similar carve-outs.