Wildlife managers need to establish proper management units based on the biological organisms and/or habitats of interest, and management entities should correspond to the spatial scales of the management units. An expanding management spatial scale is associated with an increasing number of legal requirements and larger management entities, which result in a complicated system. For example, to eradicate the plum pox virus, the roles and responsibilities of national and local governments are clearly demarcated, with small gaps between management and administrative units. Conversely, domestic quotas for the Pacific bluefin tuna, which has a reduced stock abundance, are determined according to strict international fishing regulations. Only recently have rational allocation methods for coastal and offshore fisheries been examined; however, the spatial influences of the entities that manage these fisheries correspond to the ranges of the managed fisheries. Wild populations of the great cormorant and sika deer are distributed widely across municipal and prefectural boundaries. These populations have been culled as part of nuisance control by municipalities and prefectures. However, the management spatial jurisdiction and the roles and responsibilities of each municipality and prefecture are not clearly defined. To address this issue, nuisance control by municipalities should be the top priority, and population control by prefectures should be conducted in cooperation with the relevant municipalities under the subsidiarity principle.