Approximately 5,000 wild boars and 4,000 Sika deer are annually culled on Tsushima Island to prevent agricultural, forest, and ecosystem damages. In Japan, unlike western countries, eating wild game is not common. According to a web-based questionnaire survey on the perception of game meat, over 50% of respondents had concerns regarding the hygienic status of game meat. Wild boars (n = 78) and Sika deer (n = 8) originating from Tsushima Island were subjected to microbiological testing. The meat was evaluated for total viable count (TVC) and total coliform bacterial count (TC), Salmonella spp. and enterohemorrhagic Escherichia coli (EHEC). Pork (n = 16) and chicken (n = 16) samples obtained from retail shops were also examined for comparisons. TVC and TC of wild boar and deer meat were significantly lower than those of pork and chicken (p < 0.01; Steel–Dwass test). Salmonella spp. were detected in 50% of chicken samples and 1.28% of wild boar samples. Salmonella spp. were not detected in either pork or deer. EHEC was not detected in any of the study samples. Our study clarified the hygienic status of wild boar and deer meat from Tsushima Island and demonstrated that the status was comparable to that of retail meats. School lunch service centers on Tsushima island decided to provide dishes using deer and wild boar meat beginning from 2017. This decision is an important step for recognizing deer and wild boar meat as local resources.