Seaports are under high-speed developing and booming with the extend of the facilities and equipment to support the port activities and industry’s needs. It may bring environment destruction due to the change of the environmental conditions, likes forests, soils, water, and air. Therefore, this paper aimed to analyze the negative environmental impact due to seaport activities in Malaysia. The priority dominant factors are determined through analytic hierarchy process (AHP). Malaysia Port is selected as case study and 20 respondents are selected from virous department based on their expertise. Pari-wise comparison survey is used to collect data. The results shown that the negative environmental impact’s main elements are water (0.451), noise (0.262), organism (0.181), and air (0.106). Meanwhile, the toxicity is the prominent negative environmental impact’s sub-element of port activities, which scored 0.241, followed by interfering communication (0.142), and smell (0.134). The CR values are less than 0.1 and are considered acceptable. Hence, the outcome of the paper stimulated public awareness toward environmental protection. The development and expansion of seaports must consider environment conservation and preservation, and it cannot bring irreparable sequelae to the earth.