Surveillance is critical for both early detection and a timely public health response to infectious diseases. Electronic information systems have been widely adopted by pharmacies in Japan. The aim of this study is to evaluate the feasibility of using prescription data for influenza surveillance in Japan to facilitate the development of a daily reporting system. This is a retrospective study using questionnaires mailed to pharmacies in Sakai City, Osaka, Japan in October 2007. The total number of prescriptions for oseltamivir and zanamivir and the number of influenza cases reported by sentinel surveillance in Sakai during the investigation period showed excellent correlation, with a correlation coefficient of 0.954. Further analysis showed that the data from as few as eight pharmacies result in a correlation coefficient of 0.9. These results demonstrate the feasibility of such a system and that pharmacy prescription data are a very useful indicator of sentinel surveillance for influenza.