Sika deer [Cervus Nippon] has drastically increased in abundance in Japan and deer population has affected agriculture and natural vegetation. Yakushima island was designated a world heritage for a rich flora and a unique forest. An overabundant sika deer population has inflicted serious damages on the forest vegetation. Sika deer has a small home range and the density of sika deer varies within the island. The adequate density of sika deer that prevents forest damage is unclear and may change with location. We make a mathematical model for sika deer population dynamics in consideration of uncertainties in population size estimation, population parameters and yearly changes of these parameters. We divided the island into 6 areas designated as deer density and hunting units and expect rare migration of deer between these areas. Using numerical analyses, we obtained required catch amount to decrease the population density in each area. If sika deer have been harvested on a level with harvests in 2010, we evaluated the deer population could be controlled in a few areas. Because of few harvests in 2010, population has increased in precipitous central area. The catch of deer must increase twice in order to control the total population in Yakushima Island. We need 40 fold larger catch than the catch in 2010.