Primary source info: Application Form for NJ preregistry of fingerprints
No matter where you are in Japan, if you want to play ball and preregister your biometric data, go to Tokyo. More on the difficulties involving that procedure here, from somebody who made the trip from Kobe and had a pretty lousy time once there.
Never mind–even permanent residents are still gaijin and potential terrorists, so lump it. It’s for our safety–“our” especially meaning us “kokumin”. How many more hoops will Japan make its residents jump through before it realizes this will lead to an exodus of business and money?