OBJECTIVES From April 2013, the method of calculating the prescription rate of generic drugs in Japan was changed and protected brand name drugs were excluded from the denominator. In the case of Japan, which does not have a reference pricing system, it is thought that this will lead to a change in prescriptions toward protected brand name drugs rather than drug substitution to generic drugs. The objective of this study is to clarify the trends in relation to the prescription of generic drugs, through the use of administrative data on a nationwide level. METHODS We used survey data from dispensing pharmacies from April 2012 to March 2014. As a comparison, we used the prescription data of 1139 acute care hospitals in which incentive measures for drug substitution to generic drugs had not taken place during the same period. The medical products in question were drugs for diabetes and hypotensive drugs. For data analysis used SQL Server 2008 R2 and R. RESULTS As the dispensing pharmacy receives additional compensation based on the rate of generic drugs dispensed by that pharmacy in the most recent 3 months, the dispensing rate of generic drugs will have a direct impact on their business. The change in the method of calculating generic drugs has a major impact on the dispensing pharmacies, and in this study we have shown the possibility of dispensing pharmacies shifting more to protected brand name drugs. The dispensing rate of generic drugs by acute care medical facilities has always been low, and thus the impact of the change in calculation of the dispensing ratio is correspondingly low. CONCLUSIONS The results of this study show that when encouraging drug substitution to generic drugs as a policy to reduce drug expenditure, it is necessary to consider measures in relation to the shift to protected brand name drugs.