Have you encountered discrimination or prejudices in Japan ?

[JimmySeal]

this may surprise you,but 90% of all deeds(at least in the south) have a clause saying non-whites cannot buy the house in question. They ignore it, and are trying to get rid of it, but if one wanted to, they could use race as a factor and it'd hold in court. Always read the fine print.

Yeah, southerners do a lot of racist things, but they are still breaking US law if they discriminate against someone in a housing transaction, so that nullifies whatever racist scribblings are on the deed. I refer you to the Federal Fair Housing Act of 1968:
http://www.usdoj.gov/crt/housing/title8.htm
http://www.hud.gov/offices/fheo/FHLaws/
"It shall be unlawful to refuse to sell or rent after the making of a bona fide offer, or to refuse to negotiate for the sale or rental of, or otherwise make unavailable or deny, a dwelling to any person because of race, color, religion, sex, familial status, or national origin."
Again, I'm not too clear on Japanese law, but I'm pretty sure there's something like that somewhere.

Ok, let me pose this to you: You are in Russia, you are an officer of the law. You happen to see a very dark skinned man walking down the street. Russia is predominantly white, and you see he cannot speak Russian. Would you not in the least bit go over and at least ask him, if not check his passport, if he was there legally? I don't think anything when a cop asks a Mexican for his greencard, because they have a history of coming illegally.

Good god, man. And what if every police officer in Russia took that attitude and a dark skinned man, who was there for completely legitimate reasons, was stopped three times a day for every day he was in the country? Talk about an unfriendly welcome.

Here's the thing, I didn't move the goalposts. I gave an example of how they are going to phrase it if you call them on it and it goes to court.

Glenski said they can't refuse real estate legally, and you said they can. Even if it holds up in court, that doesn't make it legal, so you are wrong.

That is my point, a privately owned business/landowner can refuse anyone they want.

Wrong. See above.
The real estate market, along with many others, is tightly regulated by strict laws. It's not a free-for-all.