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There is a distilled version of the laws available for US Military personnel or some expatriates forum:
Owning Pets Animals in Japan
Information on the rules and regulations related to owning and caring for cats, dogs and other pet animals in Japan...
Most municipalities in Japan require a new pet dog to be registered within 30 days from the date of ownership. Registration is carried out at the local municipal office or ward office in the municipality in which the owner resides. In most cases, proof of identity of the owner is required; check with the local office for any additional document requirements. Once registration is complete a dog licence tag is provided, which should be attached to the dog's collar.
Any change in address, ownership or in the event of the dog's death must be reported to the ward office. In addition, the municipality can assist with proper disposal of deceased dogs.
Buying Pets
Not all apartment buildings accept pets. Before purchasing a pet, check the lease agreement, or consult the landlord.
Vaccinations
Dogs must be vaccinated against rabies each year between 1 April and 30 June. Also, newly acquired dogs must be vaccinated within 30 days of ownership if it is over 90 days old. The rabies vaccination tag should be attached to the dog's collar.
Other vaccinations are not required by law; however, they are recommended for the continued health of the dog. One exception is for imported dogs, which must be up to date with vaccinations.
For further information, see the section on Importing Pets & Animals to Japan
Dogs in Public Places
Dogs must be kept on a leash when out for a walk. Dogs are generally not allowed in restaurants and shops. Small pets are allowed on public transport in a carrier. Guide dogs are permitted on public transport.
The owner is responsible for cleaning up after their dog.
There are no restricted dog breeds in Japan.
Information for Cat Owners
The Tokyo Metropolitan Government recommends that cat owners:
Keep their cat inside the home Sterilise/neuter/spay the cat. Some municipal offices help pay part of the fee for neutering the cat Use a collar marked with the address and name of the owner In addition, the local municipal office can assist in the proper disposal of deceased cats.
Vaccinations for cats are not required by law; however, they are recommended for the cat's long-term health.
Other Pet Animals
Dogs and cats are the most popular pets in Tokyo. However, due to many landlords restricting dog and cat ownership, smaller pets are also popular including fish, turtles, hamsters and ferrets. Certain animals are categorised as special animals and require permission to own in Japan. These restricted special animals are generally those that can attack people such as monkeys, eagles, hawks, crocodiles and snakes. Permission to own these animals is required from the local municipality office.