The Great East Japan Earthquake and the successive accidents at the Fukushima Daiichi Nuclear Power Station are stark reminders of the importance of energy, which is the basis of economic activity and national governance. Urgent responses have been conducted since March 11, 2011, including controlling the consequences of the nuclear accident, dealing with the short-term power shortages, and a comprehensive review of Japan's long-term national energy policy. Nationwide discussions and reviews of these issues are still continuing. Even today, more than 2 years after March 11, many problems remain unsolved and Japanese society has to face uncertainty and challenges about its energy future. In the current difficult situation, Japan needs to achieve “3Es (energy security, environmental protection, and economic efficiency)” plus “S” (safety) and “M” (macro economy protection) simultaneously, taking account of the new realities following the Fukushima accident. This paper tries to identify the energy-related challenges that Japan has to face and tries to recommend the concept of the “energy best mix policy” for Japan, by describing the present status of energy issues in Japan and the national debate on energy policy.