Infectious diseases at the wildlife-livestock-human interface have become a crucial issue, and evidence-based measures are growing increasingly important. One countermeasure against animal diseases in wildlife is using fencing to contain and reduce disease spread and transmission rates between wild populations; however, quantitative assessments on fencing are rare. Moreover, existing research on fencing has highlighted knowledge gaps on the social and ecological aspects relevant to the use and design of fences. To control the spread of classical swine fever, fences were installed from the east to west in Gifu Prefecture, Japan, by March 2019, with the aim of restricting wild boar movement. To clarify the process of installation and maintenance of the fences, we conducted semi-structured interviews with prefectural government officers in Gifu Prefecture. Additionally, we installed infrared-triggered cameras at fence locations with and without gaps to evaluate the fence permeability of mammals. We used a generalized linear mixed model to evaluate the relationship between the presence of gaps and the relative abundance and permeability of each mammal. Our findings showed that the occurrence of gaps was inevitable during the installation and management of wide-area perimeter fence in Japan, partly because of social factors. For example, fences could not be installed on roads that were frequently used by residents and were not adequately maintained owing to budgetary reasons in some cases. Analysis of footage from the infrared-triggered cameras revealed that several mammal species crossed the fence at gaps and even had the ability to cross the gapless parts of the fences. Wild boars crossed through the gaps regularly. It is possible that Sika deer, Japanese serows, raccoons, Japanese badgers, raccoon dogs, Japanese macaques, and feral cats crossed through fence gaps because their relative abundance was high at gap locations. In contrast, Japanese hares slipped through the fence mesh rather than crossing through the gaps. In conclusion, we suggest that coordination and collaboration among related parties, a sufficient supply of fence materials, and securing a budget for fence maintenance are important for fence installation and maintenance. Furthermore, as fence gaps are inevitable, technical development of countermeasures for these gaps could be effective.