IIRC the majority of foreigners in Japan are from other Asian countries and experience varying degrees of discrimination despite many of them being able to at least outwardly pass as Japanese. According to the latest info in Wikipedia, the top countries are China, Vietnam, Korea, Phillippines, and Brazil.

Brazil is an interesting one, because a significant number of "Brazilians" in Japan are supposedly descendants of Japanese who had immigrated to Brazil, but then came back. But even they experience degrees of discrimination despite being ethnically Japanese.

Anecdote, but my Japanese American friend (ethnically 100% Japanese but born and raised in the US, and pretty much culturally 90%+ American) went back to Japan. He too experienced discrimination.