After the launch of governmental financial support for the development of a regional suicide prevention programme, ‘Emergency Fund to Enhance Community-Based Suicide Countermeasure’ in 2009, suicide mortality rates in Japan have decreased from 25.7 (in 2009) to 16.5 (in 2018) per 100,000 population. Therefore, to explore the effects of governmental financial support on suicide mortality rates in Japan, the present study determined the relationship between the trends of empirical Bayes standardised Mobile Ratio of suicide mortality ratio in all 47 Japanese prefectures (EBSMR-RR) and the execution amounts of 10 sub-divisions of ‘Emergency Fund to Enhance Community-Based Suicide Countermeasure’ using stepwise multiple regression analysis. The female EBSMR-RR was only significantly/inversely related to the municipal ‘development of listeners and leaders’, whereas male EBSMR-RR was significantly/inversely related to prefectural ‘enlightenment’, and ‘intervention models’, but significantly/directly related to prefectural ‘personal consultation support’. The present findings suggest the inverse relationship between financial support and the suicide mortality rates in Japan. Furthermore, the independent factors in the reduction of suicide mortality rates between males and females provide important information for planning a scientifically evidence-based and more cost-effective regional suicide prevention programmes.