Purpose: We examined the modifying effect of cigarette smoking (i.e., smokers vs. non-smokers) on the association of organizational justice (i.e., procedural justice and interactional justice) with serious psychological distress (SPD) in Japanese employees. Methods: Overall, 2838 participants from two factories of a manufacturing company in Japan completed a self-administered questionnaire comprising the scales on organizational justice (Organizational Justice Questionnaire), smoking status, psychological distress (K6 scale), demographic and occupational characteristics (i.e., gender, age, education, family size, history of depression, chronic physical conditions, occupation, and work form), and other health-related behaviors (i.e., drinking habit and physical activity). Multiple logistic regression analyses were conducted. In a series of analyses, interaction term of procedural justice or interactional justice with smoking status was included in the model. Results: After adjusting for demographic and occupational characteristics as well as other health-related behaviors, low procedural justice and low interactional justice were significantly associated with SPD (defined as K6 ≥ 13). Furthermore, marginally significant interaction effect of procedural justice with smoking status was observed. Specifically, the association of low procedural justice with SPD was greater among smokers [prevalence odds ratio 7.13 (95 % confidence interval 3.25–15.7) for low vs. high procedural justice subgroup] than among non-smokers [prevalence odds ratio 2.34 (95 % confidence interval 1.52–3.60) for low vs. high procedural justice subgroup]. On the other hand, interaction effect of interactional justice with smoking status was not significant. Conclusions: Cigarette smoking seems to have a harmful effect on the association of the lack of procedural justice with SPD in Japanese employees.