This study sheds new light on nuclear risk governance from a sociological perspective by analyzing cases of post-Fukushima controversies on nuclear safety and nuclear emergency preparedness in Japan. By critically analyzing how the three risk-related concepts and methodologies, namely, probabilistic risk assessment, safety goals, and the System for Prediction of Environmental Emergency Dose Information, have been interpreted, implemented, and/or abandoned before and after the Fukushima accident, this study identifies three common features that characterize Japan’s nuclear risk governance: avoiding critical conflicts, proclivity toward automated decision making, and strategic overlooking of “uncomfortable knowledge.” These features all involve ignorance of the dynamic nature of safety where addressing uncertainties, heterogeneous knowledge, and incommensurable values can be key for continuously reviewing the existing edifice of safety. By elucidating why such ignorance persists in Japan despite the post-accidental drastic reform, the authors both articulate the deep-rooted structure that underlies it and reflects the societal and historical context, and eventually conceptualize this ignorance as “structural ignorance” of expertise in nuclear safety controversies and policy processes. The results also provide direction for further research to solve this structural problem.