Objectives: Presenteeism refers to the condition of working while having health problems and can be one of the perspectives to assess the incompatibility between workers and their jobs. The purpose of this survey was to find out what kind of occupational health issues can be detected by occupational physicians’ interviews focusing on presenteeism. Methods: We conducted interviews with workers suffering from presenteeism in a food manufacturing company. The Work Functioning impairment scale (WFun) was used as the indicator of presenteeism. We discussed the occupational health issues and the necessity of additional interventions. Results: Thirty-nine workers with WFun score of 21 or higher were interviewed, and we have found nine cases in need of support. The workplace issues were structured into four categories: (i) health problems that are difficult to identify through health checkups, (ii) health problems missed by the stress check program, (iii) health problems caused by workload that cannot be identified by workplace patrols, and (iv) health problems that are not considered because they do not require support. Conclusions: We discovered new workplace issues by interviewing workers suffering from presenteeism.