In recent years, the impact of tourism on socioeconomic structures has attracted the attention of the Japanese government. To plan and implement effective tourism policies and strategies, it is important to understand the basic characteristics of tourism resources in a given region. Tourism resources have been regarded as one of the most important indices for evaluating the tourism potential of a region and analyzing tourism phenomena. However, previous studies on tourism regions in Japan were based on limited resources and analyses have been largely qualitative. Therefore, this study focuses on a statistical analysis of substantial data, such as the distribution of tourism resources, to clarify the regional characteristics of tourism resources in Japan. First, the number of tourism resources, which are assigned a weighted value on the basis of an evaluation ranking determined by the Japan Travel Bureau Foundation, is calculated for each prefecture. The results of the statistical dispersion show that, among prefectures, there are great differences in the quantities of each type of tourism resource. Next, the prefectures are classified into four regional clusters based on similarities of location quotients. The first cluster is abundant in natural landforms and is mainly located in eastern Japan. The second cluster predominantly consists of elements concerning surface water such as lake water and river water and is composed of prefectures at various locations around the country. The third cluster, composed of prefectures in the metropolitan areas of both eastern and western Japan, has extensive urban cultural resources. The fourth cluster primarily contains important natural and cultural components, which are closely located along the Seto Inland Sea and in southwest Japan, including Okinawa. Finally, to analyze the regional attractiveness of each prefecture, the coefficient of specialization and the weighted number of the resources are compared to ranking data on tourist arrivals and projected destinations of domestic tours. The results show that popular tourist destinations have high values in the dimension of the number of tourism resources, and these regions are divided into two types with high or low specialization. In conclusion, the distribution of tourism resources determines the characteristics of each prefecture as a tourism region and makes a difference in the regional attractiveness of prefectures. The comprehensive analysis of a wide variety of tourism resources is effective for identifying the regional differences of tourism resources and reinforcing the findings of classifications of Japan's tourism regions provided by prior studies.