Thanks to all for the feedback. Based on that, and my Yokohama colleagues thinking this was likely a legitimate encounter (no recent news reports of fake cops, etc.), and that nothing more was done than my passport being examined, I'm leaning towards this indeed being a legitimate police stop. Somewhere in the back of my mind I assumed that any such stop would be done by uniformed police so I'm sure having it done by plainclothes officers threw me a bit.

I'll continue to carry my passport as I always have (in my shirt pocket, with the added bonus that I always know where it is) and suggest that other foreigners always have theirs with them, as required when visiting Japan. A 3 minute stop to have a few passport details written down by police is nothing compared with what I assume the hassle could be if one was stopped and didn't have their passport with them.

This has done nothing to detract from my love of this country. I was originally supposed to remain in China for the weekend and when those plans were cancelled and I had the chance to come to Japan early and spend time with my colleagues/friends, I jumped at the chance. Staying in a tiny Toyoko Inn hotel room and bar hopping in Yokohama on a Saturday night beats the hell out of sitting in a fancy hotel in Qingdao.