To achieve the sustainable development goals (SDGs), all countries' efforts are essential, and each country needs to recognize their level of achievement in terms of the SDGs, identify the goals and targets that require more effort, and build more effective and well-performed governance systems to accelerate their efforts toward achieving the SDGs. This study identifies different governance system structures for achieving the SDGs and the challenges they face in improving their performance using a new matrix tool to evaluate governance systems for the SDGs. We use Japan and Indonesia as case studies to provide perspectives from countries at different levels of economic development. The results show that the governance systems for the SDGs are structurally and functionally different in the two countries, which face different challenges. Japan has relatively well-structured "vision and objective setting", "research and assessment", and "strategy development", but faces challenges in relation to "implementation" and "monitoring, evaluation, and review", while Indonesia has relatively well-structured "research and assessment", "strategy development", and "monitoring, evaluation, and review." However, Indonesia faces challenges in relation to "vision and objective setting" and "implementation." We found that the differences in the governance systems for the SDGs have arisen in relation to three key elements: differences in the development of governance systems for the SDGs, differences in the lead ministries, and the existence or otherwise of a supportive legal framework. We argue that the proposed matrix tool is useful in identifying the structure of governance systems for the SDGs and the challenges that must be overcome to improve the performance of these systems. However, some analytical limitations must be overcome before the tool can be applied to other countries.