Their trains are safe, but they also have 2X the national suicide rate as Spain, which amounts to about 17000 more deaths per year. I'd attribute a big chunk of that to their work culture treating people like machines, whereas Spain's work culture tends to lean towards treating people like humans.

That isn't an excuse for railway mishaps, of course, but I'm just trying to de-romanticize Japan as some kind of magical perfect place. It's not. They might have gotten their railways right, but they have massive safety issues around mental health.