Energy analysis results confirmed that abandoned rice fields provide a good opportunity for japan to fulfill its E-3 target by producing ethanol from high-yield rice feedstock. However, to be a viable alternative, a biofuel should not only provide a net energy gain and reduce the emissions of polluting gases, but also be ecologically and economically competitive. Thus, an integrated ecological-economic evaluation was done to determine the viability of the process, the opportunity cost of biodiversity loss and the quality of the energies consumed and produced. The results showed that although ethanol from high-yield rice has a net energy yield, it is currently neither ecologically nor economically feasible to use it to replace gasoline as a transport fuel in Japan. There is a positive effect in that polluting gas emissions are reduced, but this benefit is too small to change the large negative balance in both the emergy and economic accounts. Furthermore, converting an abandoned rice field to the cultivation of intensified high-yield rice feedstock could have a large negative effect on biodiversity at both genetic and species levels, which if fully realized, would be over 300 times the ecological economic value of the rice-ethanol output. (C) 2012 Elsevier Ltd. All rights reserved.