In this study, we evaluated the microbial safety of Pangasius fish at two companies along the Vietnamese Mekong Delta. A microbial assessment scheme was used to diagnose the actual microbiological performance of implemented food safety management systems. The results showed that the microbial safety level profiles were the same at levels 1–2, indicating a poor-to-moderate food safety output of these companies. Microbial quality parameters including total mesophilic counts, Escherichia coli and coliforms, Staphylococcus aureus, and pathogens Listeria monocytogenes and Vibrio cholerae were not in accordance with the microbiological reference standards. Even though the quality of the raw Pangasius fish originating from the two companies was dissimilar as influenced by microbial ecology, the similarity in the microbial safety profiles of the two companies revealed the necessity of validating the efficiency of food safety management systems to improve the safety of the fish product.