The Japanese Animal Quarantine Service (AQS) is the official source of information regarding the import and export of pets in Japan. The full procedure with time-lines is outlined in their very helpful English website found here.

It is imperative that persons who wish to import their pet to Japan consult the AQS website and make the proper coordination directly with the AQS in order to avoid any misunderstandings. The personnel in AQS have proved to be very helpful and they encourage direct communication through this site

Check with your airline for the terminal at which you will arrive. Other phone numbers and AQS offices around Japan are listed on their website. Note that due to strict quarantine laws of Japan, AQS is unable to grant exceptions and that animals which have not met all requirements as described on their website are subject to being held for extended periods of quarantine, or possibly deported back to the origin of the flight.