The goal of this study was to examine the current Japanese surgical payment system from the viewpoint of resource utilization. We collected data from surgical records in Teikyo University's electronic medical record system from April 1 through September 30, 2013. We defined the decision-making unit as a surgeon with the highest academic rank in the surgery. Inputs were defined as: 1) the number of medical doctors who assisted surgery and 2) the time of operation from skin incision to closure. An output was defined as the surgical fee. We calculated each surgeon's efficiency score using the output-oriented Banker-Charnes-Cooper model of data envelopment analysis. We compared the efficiency scores of each surgical specialty using the Kruskal-Wallis and Steel methods. We analyzed 2,825 surgical procedures performed by 103 surgeons. The difference in efficiency scores was significant (P = 0.0001). The thoracic surgeons were the most efficient and were more efficient than plastic, obstetric and gynecologic, urologic, otorhinolaryngologic, orthopedic, general, and emergency surgeons (P < 0.05). We demonstrated that surgeons' efficiency in operating rooms was significantly different among surgical specialties. This suggests that the Japanese surgical reimbursement scales fails to reflect resource utilization.