To evaluate the utility of body mass and body size (hind foot length and jaw length) as an ecological indicator in sika deer, we analyzed the time-series data of the measurements in three populations on Shiretoko Peninsula, Hokkaido, Japan, where density levels were different. We used GAMM and GLMM to detect changes in body mass at the capture year and hind foot length and jaw length at the birth year (cohort) reflecting density effects. After two populations reached a carrying capacity (K), they have been maintained at a low density by intensive culling, while a population has been maintained below K by long-term culling. For the population below K, the body mass for all sex-age classes, hind foot length for fawns, and jaw length for adult males decreased. For two population that reached K, the body mass for fawns and adult males, hind foot and jaw length of adults (male and female) decreased, while hind foot and jaw length for fawns increased after culling. These findings suggested the rank order of responses to density as follows; fawn> adult males> adult females and body mass> hind foot length or jaw length. Hind foot length for fawns is an important ecological indicator for detecting early stage of population increase in sika deer because it is sensitive to changes in density and could be accurately and easily measured in the field. In addition, understanding the rank order in a series of ecological indicators is useful in evaluating the population condition.