Background: The annual rabies vaccination coverage in dogs among 47 prefectures in Japan has been reported to range from 42.3% to 92.4%, and the overall coverage has been steadily declining. Given the presence of unregistered dogs and the small number of stray dogs, the true vaccination coverage is likely to be even lower. Methods: We conducted a cross-sectional survey of dog owners to identify the owner characteristics associated with dog rabies vaccination. People in Japan who currently own dogs were recruited and answered a questionnaire consisting of four sections: (i) demographic characteristics, (ii) education history associated with medicine, (iii) factors related to veterinary services, and (iv) dog characteristics. Results: A total of 534 dog owners covering 629 dogs were surveyed. Vaccination within the prior 12 months was the major outcome (56.1%). The associated variables were (a) owner education level, (b) knowledge about mandatory vaccination, (c) having a family veterinary clinic, (d) frequency of visiting a veterinary clinic, and (e) having ever been advised to vaccinate their dog. Conclusions: Although causality cannot be implied, our findings indicate improving owners’ knowledge about mandatory vaccination, facilitating attachment to a veterinary clinic, and veterinarians providing vaccination advice might increase the uptake of dog rabies vaccination. The finding in Japan did not deviate from Asian and African countries with rabies, and the sample estimate of annual vaccination coverage was lower than the reported estimate among registered dogs.