[bELyVIS]

I used to get stopped all the time in my neighborhood, sometimes by the same cop, and asked for my gaijin card. They also searched my apartment when I was at work (building super let them in) and stationed a officer outside my apartment for several months and I was never told why. My translator at my company called them to ask and all they would say is " He is a person of interest". Of interest of what? The only we could guess was that some crimes were being committed and since I was the only foreigner in my neighborhood I was a person of interest.
Japanese law forbids discrimination, but it is only on paper and real life is different. Japan is still getting accustomed to having foreigners living there and their culture makes them suspicious of us so I didn't really take it too personally. I think this is changing now.
Just stay out of trouble and have all your papers and visas in order and you will be fine.