Purpose Shared decision-making (SDM) has only lately begun attaining recognition from the Japanese medical community. The purpose of this study was to create a Japanese version of the SDM-Q-Doc, which is a scale that measures SDM from the perspective of physicians, and to clarify its psychometric characteristics and identify the issues and factors that affect SDM. Methods The participants were 23 physicians and 130 patients who visited primary care clinics in Japan for the first time. Immediately following physician-patient interviews, the Japanese version of SDM-Q-9 and SDM-Q-Doc were administered to patients and physicians, respectively. For convergent validity, physician confidence in the medical interview (PCMI) was used. After the determination of internal consistency and validity of the SDM-Q-Doc, the relations among each item of SDM-Q-Doc, SDM-Q-9, physicians' sociodemographic attributes, and a presence or absence of nurse's attendance during outpatient consultation were assessed by a multiple regression analysis and structural equation modeling (SEM). Results A factor analysis confirmed that the Japanese version of the SDM-Q-Doc displays a one-factor structure with a high internal consistency (Cronbach's [alpha] = 0.87, [omega] = 0.88). The correlation between the PCMI and SDM-Q-Doc confirmed an appropriate convergent validity (r = 0.406; p Multiple regression analyses showed that the attendance of a nurse during consultation significantly affected one item of the SDM-Q-Doc, which in turn affected one item of the SDM-Q-9. SEM showed a good fit of model for these three items. Conclusion The Japanese version of the SDM-Q-Doc's internal consistency and validity in the outpatient medical consultations in Japan were confirmed. Further, this study suggests the role of a nurse's attendance during a physician-patient consultation on facilitating the SDM. Further, using the Japanese version of the SDM-Q-Doc will promote communication skills training for medical professionals by checking the quality of SDM.