There were a lot of sweeps coinciding with that. Shibuya, Roppongi, Ueno, and Kinshicho. They went through and grabbed every single foreigner. They were very quiet and very effective. I got caught up in one going through Shibuya once, but of course I am legal so I was quickly released.
Another story — which may be an urban legend, but I have heard from several sources over the years, so maybe not — was that within a week after Sept. 11, 2001 The JNP had rounded up between 500 and 1000 Muslims who were suspected of having Islamist sympathies — including, be it noted, several popular prayer leaders — and quickly and quietly deported them.
Attempts to spark outrage in the media were met with utter indifference and stony silence by the government. What little the public saw or heard, they obviously approved.
I was living in Osaka on 9/11 and working in Amagasaki. I remember hearing the same thing, about the muslim deportations, both from my co-workers as well as there being a few short stories about it on the radio and television news at the time; but, those quickly went away.
Japanese society, as a whole it seemed, recognized the threat and decided to eliminate it in the quickest and quietest way possible. No fanfare, no protests, just sent them away.
Jeez, I miss that about Japan.