Although Japanese companies are reconstructing their enterprise system by using Enterprise Resource Planning (ERP) packages and are implementing e-business system, from management level and overall viewpoints these implementations are not done well. They lack Enterprise Architecture approach. Recently, Japanese companies are needed to innovate their business models to break through the Japanese deflation economies. To be realistic, this approach is imperative for them. The purpose of this paper is to clarify issues when they confront e-business system implementation from Enterprise Architecture viewpoint and to propose directions for their problem solving.