Although the relevant standards, technical innovations, international rules, and safety-related regulations enforce the shipbuilding industry to improve the design and structural quality of the merchant ships, there are still many design-based failures that are being encountered by operators during the service period. Design-based failures that have an influence on the technical performance and operational efficiency cause minor or catastrophic consequences, increase human errors, and impair safety on board ships. This paper mainly focuses on examining the potential causes and effects of design-based deficiencies in ship machinery space on board merchant ships by referring to the outcomes of experimental surveys, ship deficiency reports, and marine accident statistics. In addition, a shipyard-centered information network on monitoring design-based failures is proposed for managing the gaps between designers, operators, and equipment manufacturers. It encourages the shipyard organizations to enhance the design and structural quality of the shipboard systems.