Hazard Analysis Critical Control Point (HACCP) system application is expanded to food chain from farm to table to supply safe livestock products with consumers in Korea. The objectives of this study were to analyze the HACCP operating conditions in butcher shops and to suggest for better HACCP implementation. We analyzed the HACCP inspection reports for butcher shops implemented by the Korea Livestock Products HACCP Accreditation Service from 2007 to 2009 and from 2010 to 2012 to compare the rate of HACCP non-compliances. The overall rate of non-compliances was higher in 2010~2012 than 2007~2009. The current inadequate HACCP operating level was directly related with the business size. Ninety-nine percent of the butcher shops were very small business with under 10 employees in Korea, and these small-sized businesses usually had great difficulties in implementing HACCP due to lack of technical expertise and financial resources. To overcome the obstacles and to facilitate more effective HACCP application and operation in butcher shops, government should play a leading role in developing flexible and simplified HACCP-based system which merges both the pre-requisite and HACCP principles.