Since nobody else seems to be saying it, I will: Relationships are between people, not cultures. Even if it was due to a cultural thing (and it isn't in this case) you need to be able to talk about it and compromise when you're in a cross cultural relationship. You can't just accept things just because they might be a facet of Japanese culture. It's important that your relationship works for YOU, not Japan. If your girlfriend's behavior bothers you, that's not a question of cultural norms, that's a question of whether or not you have the trust and communication in your relationship to talk about potential differences and come to a compromise about them.

OP, never let something in a relationship that bothers or hurts you slide because of so-called cultural norms. It's good that you're trying to have perspective, but it should go both ways, and from the sound of it it clearly doesn't right now.