A balance between industrial pollution and economic growth becomes a major policy issue to attain a sustainable society in the world. To discuss the problem from economics and business perspectives, this study proposes a new use of DEA (Data Envelopment Analysis) as a methodology for unified (operational and environmental) assessment. A unique feature of the proposed approach is that it separates outputs into desirable and undesirable categories. Such separation is important because energy industries usually produce both desirable and undesirable outputs. This study discusses how to unify the two types of outputs under natural and managerial disposability. The proposed DEA approach evaluates various organizations by the three efficiency measures such as OE (Operational Efficiency), UEN (Unified Efficiency under Natural disposability) and UENM (Unified Efficiency under Natural and Managerial disposability). An important feature of UENM is that it separates inputs into two categories and unifies them under the two disposability concepts in addition to the proposed output separation and unification. This study incorporates an amount of capital assets for technology innovation, as one of the two input group, into the measurement of UENM. Then, it compares UENM with the other two efficiency measures. This study is the first research effort in which DEA has an analytical capability to quantify the importance of investment on capital assets for technology innovation. To confirm the practicality of the proposed approach, this study applies the three efficiency measures to a data set regarding manufacturing and non-manufacturing industries of 47 prefectures in Japan. This study empirically confirms the validity of Porter hypothesis in Japanese manufacturing industries, so implying that environmental regulation has been effective for betterment on the performance of Japanese manufacturing industries. Another important finding is that the emission of greenhouse gases is a main source of unified inefficiency in the two groups of industries. Therefore, Japanese industries, examined in this study, need to make their efforts to reduce the greenhouse gas emissions and air pollution substances by investing in capital assets for technology innovation.