This study was performed to investigate latent problems of Hazard Analysis Critical Control Point (HACCP) prerequisite program operation at Korean slaughterhouses. We analyzed the slaughterhouses HACCP operation assessment reports implemented by Consumers Union of Korea during 2007 through 2008, and also reviewed the livestock products HACCP instruction manual published by Korea National Veterinary Research and Quarantine Service. Non-compliance rates were 14.2% of facility management and 10.9% of sanitary management at mammal slaughterhouses, and 7.4% of facility management and 6.7% of sanitary management at poultry slaughterhouses. A big obstacle to better HACCP operation was a repeated non-compliances identified at the same slaughterhouse. Twenty-six inspection items of the facility management, which were same items used for the business permission standard, is required to be amended to a safety control purpose. Sanitary management items also should be complemented to more precise contents for practical and objective evaluation.