We studied the island-wide distribution of wild Japanese macaques in Yakushima (Macaca fuscata yakui) in May 2017 and 2018. We walked 165.4 km along roads and recorded the location of 842 macaque feces. We divided the roads into segments 50 m in length (N=3308) and analyzed the effect of the areas of farms and villages or conifer plantations around the segments and also the presence of hunting for pest control on the presence or absence of feces. We divided the island into three areas based on population trend changes over the past two decades: north and east (hunting present, population decreasing); south (hunting present, no change) and west (hunting absent, no change). According to conditional autoregressive models incorporating spatial autocorrelation, only farms and villages affected the presence of feces negatively in the island-wide data set. The effect of hunting on the presence of feces was present only in the north and east and the effect of conifer plantations was present only in the west. Qualitative comparisons of the census records from the 1990s with the more recent census indicated that feces were no longer found in the private land near the northern villages of Yakushima, where macaques were previously often detected in the 1990s. In other areas, such as near the southern villages or in the highlands, macaques were detected both in the 1990s and in 2017-2018. Our results further strengthen the possibility that the macaques have largely disappeared around the villages in the northern and eastern areas. Since the damage of crops by macaques has recently reduced considerably, we recommend reducing hunting pressure in the north and east areas and putting more effort into alternative measures such as the use of electric fences.