BACKGROUND: Increasing the coverage of vaccinations recommended by the World Health Organization in the older adult population is an urgent issue, especially in the context of avoiding co-epidemics during the current coronavirus disease 2019 crisis. The aim of this study was to examine factors associated with the quality of perceived patient-physician communication and whether this variable was associated with increased odds of vaccination. METHODS: We used cross-sectional data from the Japan Gerontological Evaluation Study conducted from October 2016 to January 2017. The participants were 22,253 physically and cognitively independent individuals aged 65 or older living in 39 municipalities in Japan. Multilevel logit models were used to estimate the odds of vaccination. RESULTS: Among the participants, 40.0% and 58.8% had received pneumococcal and influenza vaccinations as per the recommended schedule, respectively. People with low educational levels were more likely to have a family physician but rate their experience in asking questions lower than those with higher educational levels. Having a family physician and high rating for physicians' listening attitude were positively associated with increased odds of pneumococcal and influenza vaccinations. High rating for patients' questioning attitude and shared decision-making, compared to an ambiguous attitude toward medical decision-making, were positively associated with increased odds of pneumococcal vaccination. CONCLUSION: The results suggest that promotion of having a family physician, better patient-physician communication, and shared decision-making may encourage older adults to undergo recommended vaccinations.