Yes. The police have very wide reaching powers.

But the foreigner has rights. He has a right to know why the officer wants to inspect his ID. He also has a right to see the police officer's ID. (Except if this is taking place at a police station).

I think it makes sense to exercise these rights and to lodge a complaint about any unreasonable ID request. Imagine if this happens to you three times. By the third time, you're going to be upset. You'll be wondering (like the OP) whether you've been targetted. You will want to persuade the police to leave you alone to do your lawful business. Well, it will be hard to make your case unless you can detail the times, places and names of officers who ID'd you and the reasons they gave for the inspections. It will be much easier to make your case if you can point to official complaints that you previously lodged.

Regarding the inspection at the shuttle bus stop -- I now understand that you were at Narita airport itself (I misunderstood before - thought you were at the Hilton hotel). The situation within "fortress Narita" is a bit special, since it is constantly threatened by domestic and international terrorists. You will notice that everyone (Japanese and foreign) goes through an inspection with ID checks before entering the airport.
If you ask "Why?" at the airport, the police officer will probably name a good enough reason. But I still think it's a good idea to ask "Why?"

I'm far from a non-resident, in fact I'm a permanent resident of Japan. This is my home I'm not visiting. I will not be treated like a second class citizen. My wife is Japanese my children are Japanese, I own property here and I work and pay taxes here. I have very compelling reasons to stay in this country. I take great offence at the likes of you suggesting "I just go home". I AM HOME.:mad:

Huh?? I (caucasion, straight male) have traveled in Japan with male Japanese and non-Japanese friends before, and I've never been stopped. Unless the OP and his partner were holding hands or kissing in public, why would anyone assume they were anything other than regular friends??

FWIW, I've never been stopped by the cops in 12 years of living in Japan. But there does seem to be anecdotal evidence that such incidents are increasing...

This thread probably has run its course. Should have started it in OMNI I suppose.
First incident happened after departing a subway in near Shinjuku station and walking onto the street. Both officers intercepted us during the daytime evening hours while walking down the street with lots of people around. It really seems like they were directed towards us to intercept us and stop us.
2nd was in Roppongi station and the only significant things is it was during the morning rush hour and tons of Japanese were flowing out of the turnstiles. After they were done talking to us they all returned to their locations. One woman put a surgical mask back over her mouth because of the fumes and they all just blended right back in. It was very spooky.
My last comment is not to tell Japan how they should or should not do things (not that they're listening anyway) but simply that it really kind of rattled us a bit since no other countries has ever done this to us.

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This thread is starting to smell like a Big Daikon. :eek: