A warehouse is more than just a place to store goods but also creates a time utility gap between production and consumption that is important in the development of trade and commerce. Malaysia has a high aspiration to be the most popular gateway in Asia. However, Malaysia Productivity Corporation has claimed that particularly in efficiency and productivity aspects, the warehouse industry is less incline to innovate and make improvement to increase. There are ten failure factors that had been identified during literature survey affecting to the warehouse operations efficiency. Therefore, this study intends to analyse and select the main failure factors that mostly affecting the warehouse operations efficiency. A Fuzzy Analytic Hierarchy Process (FAHP) technique has been used in this study to calculate the weight value of each variable through a pair-wise comparison method. The finding highlighted the four main failure factors which are ‘equipment’, ‘environment concern’, ‘special handling consideration’ and ‘human factor’ that influence directly to the warehouse operations efficiency. This paper has contributed to a new knowledge of complex warehouse operation area with recommendations action that shall be taken to manage the possible risk in future, which will also contribute to achieve the government goals.