There is increasing concern that the coronavirus disease 2019 (COVID-19) pandemic could harm psychological health and exacerbate suicide risk. Here, based on month-level records of suicides covering the entire Japanese population in 1,848 administrative units, we assessed whether suicide mortality changed during the pandemic. Using difference-in-difference estimation, we found that monthly suicide rates declined by 14% during the first 5 months of the pandemic (February to June 2020). This could be due to a number of complex reasons, including the government's generous subsidies, reduced working hours and school closure. By contrast, monthly suicide rates increased by 16% during the second wave (July to October 2020), with a larger increase among females (37%) and children and adolescents (49%). Although adverse impacts of the COVID-19 pandemic may remain in the long term, its modifiers (such as government subsidies) may not be sustained. Thus, effective suicide prevention-particularly among vulnerable populations-should be an important public health consideration.