Internal auditors play crucial role in ensuring accountability, probity and governance of public sector entities. However, the effective performance of such duties would depend on the challenges faced by internal auditors in public sector institutions. The objective of this study is therefore to examine the challenges faced by internal auditors in public sector audit in Nigeria. The study specifically examined whether independence of internal auditors, compliance with set out rules and regulations of public fund management and improper segregation of duties pose a challenge to internal auditors in public sector entities. The study adopted the survey research design the population of the study was drawn from accountants and auditors in the offices of the Accountant-General and Auditor-General of Abia State. The study employed Independent-Samples Mann-Whitney U -Test technique in testing the formulated hypotheses. The study finds out that while independence and the compliance with set out rules and regulations of public fund management pose a challenge to internal auditors of public sector entities, however, that improper segregation of duties does not pose a challenge to internal auditors of public sector entities. The study recommends that the independence of internal auditors in public institutions should be enthroned. Secondly, to ensure compliance with rules and regulations of public fund management ensured.