Standardized suicide mortality rates per 100,000 (SMRs) in Japan consistently decreased from 2009 to 2019 but increased from 2020. The causes of these temporal SMR fluctuations remain to be clarified. Therefore, this study was conducted to identify the causalities underlying the recently transformed fluctuations of suicide mortality in Japan. Monthly suicide numbers disaggregated by sex and social standing, and political uncertainty indices, such as economic policy uncertainty (EPU) and government management instability (AENROP), were obtained from Japanese government databases. Interrupted time-series analysis was performed to analyze temporal fluctuations of SMRs disaggregated by sex/social standing associated with the three General Principles of Suicide Prevention Policy (GPSPP) periods and the COVID-19 pandemic. Panel data and vector autoregressive analyses were conducted to investigate causalities from political uncertainties to SMRs. During the first and second GPSPPs (2009–2017), all SMRs disaggregated by sex and social standing decreased, whereas those of unemployed females did not change. During the third GPSPP (2017–2022), decreasing trends in all SMRs were attenuated compared to previous periods. All female SMRs, except unemployed females, showed sharp increases synchronized with the pandemic outbreak. No male SMRs showed sharply increasing at the pandemic outbreak. SMRs of unemployed males/females drastically increased in the later periods of the pandemic, while SMRs of employed and multiple-person/single-person household males did not increase during the pandemic. SMR of unemployed males was positively related to AENROP but not EPU. Other male SMRs were positively related to EPU/AENROP. On the contrary, not all female SMRs were related to EPU/AENROP. Increasing AENROP generally contributed to increasing male SMRs throughout the observation period; however, susceptibility to AENROP and/or political information might have unexpectedly contributed to suppressing the sharply increasing male SMRs induced by large-scale social shocks (the COVID-19 pandemic outbreak) in Japan.