Previous studies have indicated that spatial variation in suicide mortality is associated with area-specific socio-economic characteristics, such as socio-economic deprivation and social fragmentation. However, most of these studies have been conducted in the West and findings from Asian countries are limited. This study aims to investigate associations between socio-economic characteristics and suicide mortality rates across 1887 municipalities in Japan between 2009 and 2017. Socio-economic characteristics were extracted from the 2010 census. We used single-person households and unmarried adults as indicators of social fragmentation, unemployment rate and educational attainment as indicators of socio-economic deprivation, and population density as an indicator of rurality. Bayesian hierarchical models were used to examine associations between socio-economic characteristics and suicide risk. Higher levels of both fragmentation and deprivation were significantly associated with higher rates of area-specific suicide risk. The strongest association was seen with educational attainment as an indicator of deprivation. Socio-economic status and suicide risk varied considerably by gender and age. Our results show that there are clear geographic and socio-economic inequalities associated with risk of suicide in Japan, which vary by gender and age. Suicide prevention in Japan should particularly focus on areas with high levels of deprivation.