Hazard Analysis Critical Control Point (HACCP) is a scientific and systematic food hygiene management method that identifies and controls hazards to ensure food safety. South Korea has made the application of HACCP mandatory across all slaughterhouses to supply safe animal products and has further established and utilized a general HACCP model and standardized plan for mammal slaughterhouses. To investigate the current status of the preparation and application of HACCP plans in slaughterhouses in South Korea, surveys were conducted with HACCP teams at 30 slaughterhouses. The challenges faced were the preparation and application of HACCP plans, such as during preparation of justification documents for hazard analysis, re-evaluations, and changes in process or when adjusting and reinforcing corrective actions for repetitive deviations. Additional needs were found for the smooth application of HACCP, including the provision of standardized manuals for HACCP applications, an easily accessible platform for exchanging scientific information, provision of standardized templates, and unification of templates. Overall, challenges were particularly experienced during hazard analysis and verification processes in the preparation and application of HACCP plans. This study provides information on the current status of HACCP applications in domestic slaughterhouses and baseline data for effective HACCP application in slaughterhouses.