How to bring your pets with you to Japan?

Your pets may be imported into Japan with a quarantine of fewer than 12 hours if the following conditions are met:
STEP #1: You should ready yourself as the owner before anything else!
STEP #2: Your pet should have Pet Microchip (ISO 11784/11785)
STEP #3: Rabies Vaccinations
STEP #4: 180 days wait
STEP #5: Final Medical Documentation (Health Certification)
STEP #6: Recommended treatments and measures

The people in charge of importing pets into Japan are called the Japanese Animal Quarantine Service (AQS). They have a website with English translation. It is the best place for asking your queries, and information.
https://www.maff.go.jp/aqs/english/animal/dog/index.html