The diagnostic self-assessment was studied in two companies oriented to export of frozen Pangasius fillets. The assessment of the context, control and assurance activities, and food safety output of the food safety management system (FSMS) was performed by a self-assessment questionnaire with 58 indicators. The resulted obtained via interview provided insight into the performance of the food safety management system currently implemented at these companies. These results were also analysed the strength and weakness of the FSMS. The results show that microbial safety of final Pangasius products was reflected through the performance of FSMS. Therefore, the improvements of the FSMS implemented in these companies, mainly core control and assurance activities (i.e. hand hygiene, cleaning and disinfection, etc.), are discussed in detail.