Personally (living in Japan) I've never experienced something like this, but it does happen.
If you have enough paid vacation you could pad that period with your vacation, but it requires pre-acceptance, so cooperation from your employer. Otherwise you're into non-accepted vacation territory, which could lead to financial penalties (basically withdrawing your salary, with potential tax adjustements. They could also try to sue you, and given you're fleeing assume they'd get a default judgement for instance)
Then there's all the paperwork you actually want to have properly done by your employer. They're legally obligated to, but it's always harder if you're in adversarial mode.
All in all, you can still quit cold turkey ("bakkure"), but that's a usually a PITA. Getting a pro to negociate a clean separation will be better than just disappearing, if you're not in the mood/capacity to face your employer.
PS; There are magical words that would give any employee an immediate option to never see their employer again. I don't want them in my comments, but anyone interested will find them with a simple search.
It doesn't necessarily need their cooperation. A letter sent by registered mail saying "I am using my paid leave for x days from y day", then another one saying "I resign on y day + two weeks" is enough. Of course, people would actually need to know and be willing to use their labor rights in order to do that, which is the service that quitting agents are providing.