As a part of the Government's movement toward public reserve system which aims to achieve the food security, government purchase of rice has been discontinued since 2005 and purchase of tonbags of dried paddy and wet paddy was implemented in 2007 and 2009 respectively. Following the implementation of the public reserve system, the business environment of companies involved in the government's purchase of rice, processing and storaging has been changed giving rise to the needs for re-estimate the operating cost of government-managed grains considering such changes. The objective of this study is to estimate operating costs of government-managed grains to meet the changes in the logistics and the business environment related to the government's purchase by adjusting the current rate. This study is consisted of estimation of the operating cost of government-managed grains for the newly established sectors and the adjustment of the current operating cost of reserved grains. For the newly established sectors, it is required to calculate transportation cost and unloading rate for the purchase of tonbags as well as tonbag purchase cost and facilities usage cost related to the purchases of rice by Rice Processing Complex. Besides, the current operating cost of government-managed grains needs to be adjusted considering the changes in the economic environment particularly in the cost of storage, processing, packaging, insurance and general unloading. The result of research conducted to estimate the storage cost of government-managed grains shows that daily storage cost for one ton of milled rice(including brown rice) and rough rice was KRW 176.8 while that of paddy rice was KRW 137.6. The processing cost of government-managed rice was KRW 100,890 for milling paddy rice to processed rice, and KRW 92,719 for milling brown rice to processed rice, while packaging cost for 40 kg PP and 20kg paper of rice was KRW 9,985 and KRW 15,135, respectively. The processing cost related to the government's purchase of tonbags of rice was measured as KRW 9,102 per ton for purchase of tonbags, KRW 909 for usage cost of weighing facilities, KRW 4,425 for unloading cost at the place of purchase, KRW 1,765 for loading and KRW 3,063 for grain warehousing cost.