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Purpose: Based on Japan’s regional-industries data from 1994 to 2018, we intend to analyze and present Japanese evidence on the productivity-enhancing effects of localization economies(MAR externality) and urbanization economies(Jacobs externality), and to accumulate research evidence for comparative analysis between Korea and Japan on the effect of agglomeration economies on productivity. Research design, data, and methodology: In order to empirically analyze the impact of localization economies and urbanization economies on the labor productivity, RIETI’s R-JIP database, which provides high-quality data on 31 industries in 47 prefectures from 1994 to 2018, was used. We implement a panel co-integration test for non-stationary panel data, and estimate panel co-integration vectors. Results: As a result of the panel cointegration test, labor productivity by region in Japan has a long-term equilibrium relationship with the industrial specialization index and industrial diversity index. In the estimation result of the panel cointegration vector, In the case of manufacturing, localization economy improves labor productivity, but urbanization economies does not affect labor productivity. On the other hand, in the case of IT manufacturing, both localization and urbanization economies have a significant impact on improving labor productivity. Implications: It is necessary to strengthen manufacturing specialization (localization economies) in order to improve the productivity of regional manufacturing. In addition, in order to improve the productivity of the IT manufacturing, a policy to strengthen the localization economies is important, and in addition, a policy to expand the diversity of related industries.