Currently, most mega-public construction projects suffer from unmanaged project planning, operation, and function. Today, the lack of experience in construction commissioning is a latent problem. The purpose of the commissioning process is to verify the performance of the systems and to provide documentation evidence that all equipment and systems are installed and functioning according to the design intent, standards, and requirements of the client. Commissioning is usually misunderstood as a process performed after the completion of construction. There is no sufficient study that indicates water supply construction commissioning challenges, their causes and solutions, or how far the challenges affect sectors. The objective of this study is to assess water supply construction and commissioning challenges in the case of the Amhara Water and Energy Bureau. The questionnaire was designed to evaluate the frequency of the identified problems. The data collected from the case studies and administered questionnaires‟ was analyzed using the Statistical Package for Social Science. A Relative Importance Index was used mainly for comparing the contribution of each variable to others. Hence, this research was intended to help identify the challenges of commissioning in water supply construction and fix them with remedial action. It is also expected that, from this study, the Amhara Water and Energy Bureau will put in place appropriate measures to improve commissioning performance levels. A conceptual framework was also conducted to show the relationship between commissioning and group factors of commissioning and possible mitigation measures. Six major groups of factors affect commissioning: design change-related factors, contract- related factors, material-related factors, labor-related factors, financial-related factors, and management-related factors, respectively. The research findings showed that financial related factor ranked first with an overall score of 0.7606, material related factor was second with a total RII of 0.6944, and contract related was third with a total score of 0.6467. The remaining design change-related factors, management-related factors, and labor-related factors were ranked fourth, fifth, and sixth, with an overall RII of 0.6454, 0.6287, and 0.4552, respectively. Key words: Commissioning, water supply, construction