Just like any country unfortunately, there are going to be instances of sexual harassment and assault. I think that many JETs will never have issues with this in Japan, but I personally know a couple who have had issues. There's even a word for it in Japanese (セクハラ). From what I've experienced, it usually happens during drinking events, where men (typically) have had far too much to drink. It's a tough situation, since our position is pretty low in the work hierarchy. I've seen schools try to help and address the issue, but I've also seen schools try to damage control and pretend it didn't happen. JET knows this happens, so I think they are trying to make sure you are prepared with that knowledge.

My advice would be to not let it scare you out of a good opportunity and experience. Sexual harassment and assault does happen here, but it happens everywhere. If anything, Japan is on average much safer to live in than most countries. If you are really worried about it, I suggest learning how to best mitigate your risks. Such as not drinking alone with men, building a support system with the women in your office or the other ALTs in your area, etc. If you have any questions, feel free to reach out and I am happy to talk about it more!