Cargo operations at most commercial airports are crucial to a nation’s economy and serve as a revenue source for airlines and other stakeholders. To maximise the importance of cargo operations at airports, there is a need to successfully manage cargo distribution efficiently to reduce delivery time and costs. However, achieving efficient air cargo logistics operations is often challenging due to several factors limiting cargo processing. This paper examines the factors affecting cargo logistics management at airports in Nigeria by following the quantitative research method and surveying various stakeholders by random sampling at the Lagos International Airport through a well-designed research questionnaire. Data collected were analysed using exploratory and confirmatory factor analysis. EFA identified bureaucracy, equipment and facilities, traffic flow, and malpractices as the significant factors affecting the logistics of cargo distribution at the airport. CFA validated the statistical significance of bureaucracy, equipment and facilities, traffic flow, and malpractices as critical factors affecting the logistics of cargo distribution at the airport. It was found that bureaucracy negatively affects equipment and facilities, while malpractices negatively affect traffic flow and equipment and facilities. The findings highlight the need to incorporate real-time automation of cargo processing with equipment provision to enhance airports’ capacity for efficient air freight logistics at airports in Nigeria.