Due to economic and geographical causes, the reformation of rail freight transport is now in progress in a number of countries. Railroads are ideal for moving huge quantities of non-bulk, specialised, and bulk cargo. Malaysia's rail network has developed in comparison to other modes. However, its administration and contributions are little researched and frequently unclear in the current literature. In this country, rail is mostly used for passenger transportation, and the amount of rail freight in maritime trade is negligible compared to road freight. This scenario affects the efficacy of inter-regional and intra-regional freight delivery, diminishes the competitiveness of seaports, creates a monopoly for road freight transport, and depletes road infrastructure for extensively facilitated road freight transit. This article focuses on investigating concerns about existing rail freight transport and its improvement methods, the influence of rail freight transport on seaport competitiveness, and the relationship between rail freight transport and seaport dwell time. An exploratory factor analysis (EFA) was conducted to achieve the goals of this work. Approximately forty (40) Malaysian rail operators, their clients, and multimodal transport operators participated in the online survey. The findings indicate that the primary challenges with the Malaysian rail system are performance, transit time reliability, and capacity use. Improving the rail infrastructure will have a good impact on the service dependability, freight distribution, and operation management of a seaport. By enforcing institutional integration, expanding infrastructure support systems, and successfully managing infrastructure maintenance, the rail system may be enhanced. By synchronising seaport operation, efficiency, management, and container rotation, rail freight operations can enhance seaport transit time. To maintain trade competitiveness and provide a balanced freight distribution network, the role of rail freight must be increased.