Background The main target of tuberculosis control and prevention is to detect incident cases as quickly as possible and also to prevent the occurrence of disease. It is also the responsibility of the health facility to screen the contacts, identifying children for prophylactic therapy. However, the target is difficult to meet due to issues within health facilities that cause health system diagnostic delays. Despite this, there is no information explored why health system diagnostic delays among tuberculosis patients. Method A qualitative study was conducted by using different data collection methods and sources. Seventeen DOT providers, five laboratory professionals, six program managers, and seven Tuberculosis patients were interviewed. In addition, 22 governmental health facilities were observed for the availability of resources. Data obtained from the in-depth interviews was transcribed, coded, categorized, and thematized manually. Result Health system Diagnosis delays reasons were related with sample collection procedures, poor competency of health professionals, in addition to absences or scarcity of health professionals, medical products, and basic infrastructure. We found 18 health facilities without skilled personnel in the OPD, 7 health facilities with a broken microscope, and almost all health facilities without a separate room for sputum examination. Furthermore, 12 (54.5%) and 14 (63.6%) health facilities lacked access to water and electric power, respectively. Conclusion Many reasons for TB diagnosis delays have been identified in the study area. Poor competence of health workers and scarcity of resources were identified. Depending on the finding, we suggest strengthening the health workers’ training. Concrete strategies need to be designed to retain professionals. Training on human resource planning and budget preparation is needed for front-line managers. Managers have to work on the maintenance of diagnostic tools and facilitate transportation. The rural health facilities need to use another alternative power source.