Korea’s R&D investment has significantly increased in recent years and the quantitative outputs such as number of papers and patents have also increased with the investment. However, the quality of R&D outputs has not been fully addressed. In particular, quality of technical performance, such as the quality of patents, has attracted little attention. In this paper, a Data Envelopment Analysis (DEA) method was used to construct models for efficiency analysis of R&D investment, focused on quality of technical performance. Indices were proposed to analyze the quantitative and qualitative efficiencies of R&D investment. In order to effectively analyze R&D efficiencies, the measurement units of the input and output variables were standardized. Based on cases of livestock quarantine R&D projects of Korea, the quantitative and qualitative efficiencies of national R&D projects were analyzed and factors that would influence R&D efficiencies were identified. This paper suggests that both quantitative and qualitative efficiencies should be considered when measuring R&D efficiency. Also, it is recommended to carefully consider the characteristics of R&D projects during project selection stage.