In Japan, suicide mortality has been improving from 2009; however, suicide remains one of the leading causes of death. Although previous studies identified solid relationships between governmental financial support for social welfare systems and suicide mortality, little attention is paid to how specific regional policies, designed according to regional cultural, economic, and social welfare situations, affect suicide mortality. Therefore, the present study analyses the relationships between the regional governmental expenditure of six major divisions and suicide mortality across the 47 prefectures in Japan from 2009 to 2018 using fixed-effect analysis of hierarchal linear regression with robust standard error. The expenditure in “public health”, “police”, “ambulance/fire services”, “welfare” and “education” is associated with reduction in suicide mortality, at least in some statistical indicators, whereas expenditure of “public works” indicated the influence of increasing suicide mortality or had no effect. Welfare expenditure was the most predominantly effective among the six major divisions of regional governmental expenditure. In the welfare subdivisions, expenditure of “child welfare” and “social welfare” was effective in a reduction in suicide mortality, but expenditure of “elderly welfare” surprisingly contributed to increasing suicide mortality. Child welfare expenditure negatively impacted suicide mortality in wide-ranging generations of both males and females; the positive effects of elderly welfare expenditure reached were limited as working-age populations increased, but unexpectedly did not affect the suicide mortality of elderly populations. The relatively increasing expenditure of elderly welfare with the relatively decreasing child welfare are unavoidable due to the Japanese social issues associated with a declining birth rate and ageing population. Furthermore, the budget of that regional government that can modify its expenditure structure by making its own policies is limited since most regional governmental expenditure is composed of essential expenditure for maintaining and operating regional social welfare systems. Although severe social situations in Japan are still unoptimised, the present results suggest that scientific-evidence-based redistributions of welfare expenditure in regional governments can at least partially improve Japanese society and welfare systems.