At the landscape scale, localised culling is often conducted to achieve various deer management aims. However, few studies have assessed the effects of localised culling on deer population dynamics due to the spatially and temporally insufficient datasets of deer abundance that are derived from limited survey efforts. Here, we estimated the population dynamics of a sika deer (Cervus nippon) population in the Tanzawa Mountains, Japan, using Bayesian state-space modeling employing spatially and temporally insufficient abundance indices; we evaluated the effects of localised culling on subsequent density changes in 56 units. The responses of deer density to unit-specific culls differed greatly among units. Further, there was no correlation between the intensities of unit-specific culls and the reduction in density. Deer populations in some units tended to resist density decreases despite high culling pressure, whereas those in other units exhibited decreases in density with little to no culling pressure. Because the spatial scales of each unit were relatively small (the average size is 13.6 km2), annual density changes in each unit were largely influenced by deer migration in this estimation. The obscured effects of unit-specific culls, which were probably derived from deer migration in this case study, re-emphasize that deer migration should be incorporated into the planning of localised culling, and that management should be coordinated over a wide area transcending landscape components and land ownerships. We thus demonstrate that Bayesian state-space modeling is valuable for practical deer management programs over a large spatial scale even if different abundance indices are used.