Four years after the Fukushima nuclear power plant accident, a future portfolio of the electrical power generation mix was finally and officially determined by the Japanese Government. Opposition to nuclear power generation remains high in the Japanese public to accept the need for nuclear power given the potential for a nuclear accident in the future. In this paper, we introduce an Analytical Hierarchy Process model to evaluate the influence of two opposing risk perceptions relating to public opinion versus scientific risk measures related to the electrical generation mix. This study revealed that opposing viewpoints on safety results in choosing different generation mixes. It should be noted that the public in large chooses the nuclear-free preference that actually results in a higher number of human fatalities in the energy sector because of the statistically low accident rate in the nuclear energy generation sector, which is contrary to public sentiment in Japan.