This study focuses on implementation system of wildlife management in six prefectures of Kinki region from the view point of governmental organizational structures. The roles and relationships of relevant departments and their subsidiary bodies were clarified through interview surveys to prefectural officials, which were then classified into three types. The performances and problems of the three types of implementation system of wildlife management were identified by the interview to municipal officials in charge of wildlife management. We identified that 1) three implementation systems showed different performances and problems in their operation and cooperation with municipalities, 2) cooperation among relevant departments and their subsidiary bodies with different authorities are of crucial importance to deal with wildlife management and also to provide support for municipalities and 3) liaison and adjustment between prefectures and municipalities are important for effective wildlife management.