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Recently, nanotechnology has grown as one of the leading science technology along with other converging technologies such as biology, information, medicine etc., bringing the continuous investment of the government in nano-related field. However, it is difficult to measure and evaluate the performance of the national research and development programs because of the multidimensional character of the expected outcomes. This study aims to measuring efficiency of the national nanotechnology research and development programs using DEA model. The decision making units are nine nano-related ministries including the Ministry of Science, ICT and Future Planning. The input variables are total expenditure, number of the programs and average expenditure per program. The output variables are science, technology and economic indicator, and the combination of these outputs are respectively measured as seven different DEA cases. The Ministry of Science, ICT and Future was the first efficient ministry in total technical efficiency. Ministry of Agriculture, Food and Rural Affairs and the Ministry of Food and Drug Safety were efficient in pure technical efficiency, when the Ministry of Commerce Industry and Energy took the first in the scale efficiency. The program efficiency was affected by organizational characteristics such as the institution’s scale, the concentration of the research paper or the patent, technology transfer or the commercialization. The result of this study could be utilized in development of the policy in the nanotechnology and the related field. Furthermore, it could be applied for the modification of expenditure management or the adjustment of the research and development programs’ input and output scale for each ministry.

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