Sickness absences are a significant public health and economic problem worldwide. However, sickness absence diagnoses and trends have not been reported in much detail in Japan. This study was a retrospective cohort study. We examined data on certified diagnoses and the durations of sickness absence lasting over 90 days (long-term sickness absence) from 2009–2018 among city public servants in Japan. We found that 1) “Mental and behavioral disorders” (495.0–780.6 per 100,000 employees) was the most prevalent reason for long-term sickness absence, and “Mood disorders” (318.6–584.3 per 100,000 employees) was the most prevalent mental disorders diagnosis in each study year; 2) the prevalence of long-term sickness absence for mental disorders showed decreasing trends (781/100,000 in 2009 to 622/100,000 in 2018; [
p=
0.005, for the trend test]); 3) the trends differed by gender (
p<
0.05) and age (
p<
0.001); and 4) the duration of long-term sickness absence related to mental disorders (13.2 ± 9.0 months) was longer than long-term sickness absence resulting from all physical disorders except for diseases of the circulatory system (15.1 ± 11.6 months). Increased focus on significant depressive and neurotic disorders is needed when promoting mental health in the workplace.