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Abstract Japan is the sixth largest greenhouse gas emitter in 2016 and plays an important role to attain the long-term climate goals of the Paris Agreement. One of the key policy issues in Japan's energy and environmental policy arena is the energy system transition to achieve 80% emissions reduction in 2050, a current policy goal set in 2016. To contribute to the ongoing policy debate, this paper focuses on energy-related CO 2 emissions and analyzes such decarbonization scenarios that are consistent with the government goals. We employ six energy-economic and integrated assessment models to reveal decarbonization challenges in the energy system. The modeling results show that Japan's mitigation scenarios are characterized by high marginal costs of abatement. They also suggest that the industrial sector is likely to have a large final energy share and significant residual emissions under the 80% reduction scenario, though it is generally thought that the transport sector would have large decarbonization challenges. The present findings imply that not only energy policy but also industrial policy may be relevant to the long-term environmental target. Given the high marginal costs exceeding those of negative emissions technologies that could place a cost ceiling, further model development would be crucial. Highlights • We analyze the energy system scenarios to achieve 80% reduction in carbon dioxide emissions by 2050. • We employ six integrated assessment models to reveal decarbonization challenges in the energy system. • The model results show that the industrial sector has a large final energy share and significant residual carbon dioxide emissions under the 80% reduction scenario. • We also show that Japan's mitigation scenarios are accompanied with high marginal costs of abatement. [ABSTRACT FROM AUTHOR]