When I traveled to Japan (without any pets) the travel.state.gov website had a lot of good info.
This is what it says about pets:
"Pets: The Japanese Animal Quarantine Service (AQS)
http://www.maff.go.jp/aqs/english/index.html sets procedures for importing pets. In most instances, the process will take at least seven (7) months from the date of the first rabies vaccination before a pet may enter Japan, so advance planning is critical. More information about importing a pet into Japan is available at
http://japan.usembassy.gov/e/acs/tacs-petsi.html. More information about exporting a pet from Japan is available at
http://japan.usembassy.gov/e/acs/tacs-petse.html."