The estimated number of sika deer within the Tanzawa Mountains has decreased since the Kanagawa Prefecture sika deer management plan commenced. Meanwhile, unit-specific culling has resulted in various trends in deer density across small monitoring units. Deer abundance is usually surveyed within small monitoring units; therefore, the evaluation of deer abundance changes across the entire management area comprising individual units is difficult. We examined the relationship between deer body condition indicators and densities estimated at both individual unit and entire management scales in the Tanzawa Mountains during 2004–2015. Winter fawn body mass in the study area increased at least until 2011, irrespective of the increase/decrease in deer density in each unit. Observed variations in body mass were related to the estimated number of deer within the entire management area. Winter fawn hind foot length was not related to any density estimates. Inconsistencies between deer density changes in each unit and body mass might derive from the deer movement between units and mitigation of density-dependent food limitations caused by a reduction in the number of deer within the entire management area. We suggest that winter fawn body mass can provide additional evidence of deer abundance changes within management areas.