I’d say that visiting Japan as a trans person in terms of physical safety isn’t so much of a problem. From mine and my friends experience,* whether a trans person feels physical safety in Japan is more about income level and country of origin, rather than being trans. Tourists are well above the poverty line.
My Filipino friend who has previously lived in poverty has told me about some pretty unsafe conditions for her working the nightlife in Kabukicho. Filipino, Indian, Indonesian, Brazilian and African residents of Japan can be treated very harshly here and are more likely to be put into poorly paying jobs and have their important paperwork “forgotten” by bureaucrats so they slip through the cracks.
My Japanese friend, who is income stable, enjoys a life where he is generally out. His cis folks don’t really get the trans thing, but he’s “one of the guys” nonetheless. He doesn’t worry about his safety.
As for living here, having access to equal rights as a person aren’t good. There’s a few examples that come to the top of my head are:
- a trans man being loudly called “Miss” in the waiting room of a gynecologist (because his health insurance card requires he has the F marker on it)
- a Japanese person with an indeterminate gender eating at a local restaurant who was accosted by a Japanese reporter, “What are you? Are you a boy? Or a girl?” And the incident was broadcast on live TV
- being stuck in immigration all day because one piece of documentation says M and another says F and bureaucracy being what it is in Japan, they cannot help you unless they understand this discrepancy in your paperwork.
As a tourist, you don’t encounter these sorts of things, but as someone living here, you do. Most folks are ignorant of the issues trans people encounter day to day, but there’s a growing awareness.
The thing I would recommend for trans tourists to Japan is to, if you’re going to an onsen, check to see if it’s mixed-gender (rare) or if it has private booking times (called kashikiri). That way, you get to enjoy the onsen in peace without having to explain your gender situation to a red-faced attendant who is apologizing over and over again. It’s a pain in the ass, and not something you want to be doing on vacation, so save yourself the trouble and get a private situation with you and your friends.
TL;DR: Visiting to Japan as a trans person is, in my opinion, safe. Being a trans person who has immigrated here and doesn’t have a lot of money…that’s more dangerous.
*I cannot speak for all trans folks in Japan.

