QUARANTINE
There is a detailed site by the Ministry of Agriculture, Forestry, and Fisheries, Japan on quarantine. The URL is as follows: http://www.maff-aqs.go.jp/english/ryoko/
REGISTRATION
You must register your dog to the Minato Public Health Center. You need you bring your "Proof of Rabies Vaccination" to the Health Center and 3,000 Yen for registration fee.
For details;
Minato Public Health Center
Address: 5-16-45 Roppongi, Minato-ku
Phone #: 03-3408-6146, ext.: 317