The present research investigated the prevalence of musculoskeletal disorders (MSD) among a previously understudied group of Asian nursing professionals in a rural setting. A total of 305 female nurses (84% response rate) were recruited from a university teaching hospital in Yamanashi prefecture, central Japan. Data were gathered by means of a self-reporting questionnaire. Lower back pain (LBP) was the most commonly reported MSD, affecting 59% of all nurses. This was followed by MSD of the shoulder (46.6%), neck (27.9%), knees (16.4%) and upper leg (11.8%). Working in the surgical department was shown to increase the risk of any MSD 2.7 times when compared to nurses in the other departments (odds ratio 2.7, 95% confidence interval 1.2-6.7, P = 0.0202). Overall, our study shows that MSD are reasonably common among registered nurses in a rural Japanese hospital. These staff may also be at greater risk of suffering MSD than their city-based nursing counterparts and foreign colleagues, particularly with respect to LBP.