We examined the impact of sika deer on the physical properties of soil and the underlying mechanisms in forests on the Boso Peninsula in surveys and a field manipulation experiment. In the broad-scale surveys, we measured soil hardness, litter mass, coverage by understory vegetation, and other environmental variables likely to affect soil properties. To identify causal relationships, we performed a path analysis, model selection using the Bayesian Information Criterion, and model averaging. In cedar forests, sika deer had no effect on soil hardness or litter mass. In cypress forests, sika deer affected the soil properties indirectly by decreasing the understory cover, while they affected hardwood forests directly. Removing the understory plants preferred by sika deer in the manipulation experiment increased soil and litter erosion and soil hardness in cypress plots, but not in cedar plots. This indicates that the impact of sika deer on the physical properties of soil varied among forest types, and the change in soil physical properties reflected the formation of a soil surface crust by raindrops and soil erosion. These changes in soil properties could lead to regime shifts in forest ecosystems, which should be examined in the future.