As London and post-Koyto protocols presumably affect emission of organic waste in Korea in 2012, appropriate treatment of organic waste becomes very important. Organic wastes are regarded as non-point pollutants. It has been criticized that direct emission charges on the emission of non-point pollutants are not effective due to the high uncertainty in the relationship between pollution sources and pollution levels. This study suggests indirect emission charges on production of livestocks or consumption on foods. Furthermore, it is assumed that revenue from the emission charges will be recycled to support biogas production. Biogas can be fueled to produce energy. In order to evaluate potential economic and environmental impacts of recycling the indirect emission charges on organic wastes, a static CGE model was developed. Simulation results of emission charges on the production of livestock show that livestock, agriculture, and food industry will confront relatively high burden while emission charges on consumption of food will affect more broadly and consumers will suffer more. Production charge on livestock sector will lead to higher reduction in GDP and total expenditure relative to the consumption charge. GHGs reduction effect was higher for the consumption charge relative to the production charge. Synthetically, consumption charge on food sector is more desirable as an alternative charge for the emission of organic wastes.