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The need to eliminate bottlenecks to port operations in Nigeria was a fundamental goal of the port privatization about 2 decades ago. Current trends in ports management; however, suggest existence of numerous inefficiency challenges reflected in long ship turnaround time, increasing trend of cargo dwell time, high cargo pilferage risk rate, poor condition of port infrastructure and superstructure, multiple charges and government agencies, cumbersome cargo clearance & examination procedures, port congestion related delays particularly in Apapa and Onne ports, etc. The study identifies the decisive port-related factors constraining the flow of shipping trade in Nigerian ports using a survey to obtain data on the influence of the identified factors on the flow of shipping trade in Nigerian ports. The Principal Component Analysis (PCA) was used to analyze the data obtained. The results indicate that high cargo pilferage risk profile, long ship turnaround time and increasing trend of cargo dwell time constitute the significant port-related factors constraining the flow of shipping in Nigerian ports. It can be concluded that terminal operators should prioritize solutions to the problems of high cargo pilferage risk profile, long ship turnaround time and increasing cargo dwell time, which constitute the major constraints to the flow of shipping trade.