Public health medical laboratories are a component of the healthcare sector where clinical pathology tests are carried out on clinical samples, and test results aid in the diagnosis, treatment and monitoring of disease. It is therefore important that medical laboratories comply with international accreditation standards (ISO 15189:2012) to ensure the accuracy and reliability of test results. In South Africa, the National Health Laboratory Service (NHLS) is the public medical laboratory sector that provides diagnostic pathology services to approximately 80% of the population. In Gauteng, only eight of 24 laboratories were ISO 15189 accredited by 2018. This study investigated the possible reasons for non-compliance with the ISO 15189:2012 standard that contributed to the slow progress towards accreditation. Internal auditors who audited the Haematology, Clinical Chemistry and Microbiology disciplines in these laboratories, were asked to complete an electronic multi-response survey. They were asked to identify common non-conformance in the non-accredited laboratories, give possible reasons for non-compliance with ISO 15189:2012, and recommend ways to improve compliance with the standard. Similar non-conformance were recorded among the non-accredited laboratories and the auditors highlighted possible reasons for non-compliance with ISO 15189:2012. Challenges that were identified, included a lack of staff commitment towards quality management systems (QMS), variation in staff competencies, lack of understanding of the standard requirements, lack of QMS training in terms of implementing QMS, and low human resource capacity. Several recommendations to overcome identified challenges were cited. The findings of this study may assist public health laboratories to strengthen and advance their QMS, and to ultimately increase accredited compliance status to ISO 15189. [ABSTRACT FROM AUTHOR]