Environmental issues have become gradually important around the globe, which has increased society needs for the environment-friendly construction. In an effort to realize the environmental protection and energy efficiency, the British BREEAM has been developed, which is followed by the USA LEED, Japanese CASBEE and other national certification systems based on their own conditions. In this end, the Republic of Korea has implemented its own certification system named GBCS(Green Building Certification System) in 2002, and now actively promoted the G-SEED(Green Standard for Energy and Environmental Design) after GBCS modifications and amendments. The purpose of this study is to identify possible problems to be encountered in the process of the G-SEED for office facilities and to provide relevant solutions. In this end, three office facilities have been selected, which had obtained the G-SEED. This study has analyzed reasons of change of assessment scores between the preliminary certification and the main certification phases, has identified problems through in-depth interviews with practicing professionals(design, construction, eco-friendly consulting firm) and then has reached a conclusion for improvements. This study will be possibly used as reference materials for improvements of the green building certification system, and further detailed studies on respective parts will be required for improvements.