Sika deer (Cervus nippon) populations in Hokkaido have irrupted during the last three decades, causing severe damage to agriculture and forestry. Methods have been developed to estimate their population size on large but not on small scales. We estimated deer density using distance sampling to analyze the feasibility of employing the line-transect method in forested habitats on a management-district scale. Spotlight counts were conducted four times each year on the Iburi (IMD; 11 routes; 328.8 km total survey length) and Kushiro (KMD; 10 routes; 352.6 km) management districts in November 2013 and 2014. We observed 206 herds (302 deer) on the IMD and 680 herds (1,173 deer) on the KMD. Density estimates on the KMD, 39.6 ± 4.9 (average ± SE) in 2013 and 15.6 ± 2.3 in 2014, were significantly higher than those on the IMD, the former 8.4 ± 1.9 and the latter 4.4 ± 0.8. The line-transect method using distance sampling was useful for estimating deer density on the management-district scale. However, the large interannual variations of estimated density suggest that we have to specify the factors for annual variation in the future studies.