Large-scale decontamination work has been carried out in the aftermath of the Fukushima Daiichi nuclear power station accident in Japan in 2011. The soil that was removed and the wastes that were generated during the decontamination will be finally disposed of outside Fukushima Prefecture by 2045. To ensure successful and socially acceptable implementation of this final disposal process, it is essential to have a good understanding of what is considered important by the public. We used a choice-based conjoint analysis in the form of a web-based questionnaire to examine the relative importance of several factors in the choice of the final disposal sites of the removed soil and incinerated ash of the wastes. The questionnaires covered four attributes and 12 levels, namely the distance between the disposal site and a person’s residential area, procedural fairness (decision process), distributive fairness (direct mitigation of inequity through multiple siting locations), and the volume and radioactivity of the substances to be disposed. Responses were received from 4000 people nationwide, excluding Fukushima residents. The results showed that the respondents gave high importance to choosing sites that were far from residential areas and to the two types of fairness, especially distributive fairness. The respondents showed no preference for the volume and radioactivity. This indicates that the public cares about the fairness of the siting for the final disposal sites and feels uncomfortable with plans for a final disposal site located close to them. Distributive fairness is necessary to pursue consensus in addition to procedural fairness.