Whether you're a first-timer traveling to Japan in the near future, a long-time resident holding a working visa, or just someone who wants an extended layover on route to Peking, be aware: immigration authorities will take your fingerprints.
Beginning in November 2007 immigration will resume fingerprinting of all foreign nationals entering Japan. If you refuse to be fingerprinted, you will be denied entry into Japan.
Why? Concerns over terrorism, which is a little ironic, considering that in most instances caused by a "terrorist" in Japan, the terrorist himself was Japanese.
I'm not entirely sure about the fine lines between working visa holders, permanent residents, spouse visa holders, or Japanese citizens who happen to look "foreign". Right now all I can promise you all tourists will be fingerprinted. Be prepared to accept this if you want to visit.
Click here to view a video in which paid actors act over-enthusiastic and stupid to give immigration authorities a means to inform foreigners about these changes.
Japan did have a foreigner fingerprinting policy some years ago: read some history about it here.