Inefficient and ineffective performance audit implementation results in poor attainment of organizational goals and objectives, thereby poor organizational performance, and absence accountability. The main objective of this study is to assess the challenges of performance audit implementation in some of the selected audited public sectors in Amhara National Regional State. The factors used to assess challenges of performance audit were perceptions of public sectors auditors on the performance audit, the obstacles of the auditors in the implementation of performance audit and the performance audit challenging factors of six explanatory variables; lack of capacity building, absence of consultant recruitment, lack of awareness level, absence of pre-set goals, absence of accountability and lack of top management support were regressed against the dependent variable of performance audit ineffectiveness. The results show that performance audit takes more time and financial resources; Lack of cooperation and commitment from auditees in conducting the performance audit; Inadequate management information and Performance audit team itself lacks technical knowledge.