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This is a preliminary study on the modal split of reducing environmental contaminants to a minimum. In this paper, we focus on NO_x as a typical air pollutant and make clear the structure of energy flow with regard to freight transport using input‐output analysis. Then we present a mathematical model for the optimal modal split considering the input‐output structure of energy flow. The goal of this model is to minimize NO_x which is emitted in the processes of freight transport, energy transport and energy production subject to maintaining the status quo of freight volume transported in Japan. This model is applied to the actual freight transport problem in Japan and the validity of this model is evaluated. As the result of that, we could suggest a policy of the modal shift, which can reduce the volume of NO_x emissions in the transportation sector by approximately 30 per cent compared to the current circumstances in Japan.