The Ethics and Anti-Corruption Commission has given governors 60 days to establish an audit implementation plan.
In a statement, EACC said after conducting corruption risk assessments at various county governments, they identified weaknesses in the operation of the internal audit functions in both the county executives and assemblies.
EACC said some of the weaknesses identified include non development of policies and procedures manuals to guide internal audit processes.
The commission found that counties failed to constitute and operationalise Internal Audit Committees and Audit Committees were not holding meetings regularly.
"The Heads of Internal Audit Units reported both functionally and administratively to the Chief Officer for Finance or to the Clerks in the case of County Assemblies, in contravention of Regulation 155(1) of the Public Finance Management, (County Government) Regulations, 2015 which requires functional reporting to the Audit Committees," EACC said.
The anti-graft agency said accounting officers failed to implement Internal Audit recommendations and to develop and submit response and action plans to the chairpersons of the audit committees within 14 days.
It said Heads of Internal Audit Units and the Audit Committees failed to undertake performance appraisals to determine the effectiveness of the internal audit assurance.
"Heads of Departments and Sections are not cooperating with Internal Auditors and providing required documents, information and clarifications, or responding to internal audit queries," EACC said.
Other weaknesses are that Internal Audit Units were not undertaking risk-based audits as required and the county governments failed to adequately facilitate the Internal Audit Units to effectively carry out their responsibilities.
EACC gave governors an ultimatum to submit an implementation plan to address the challenges.
"In this regard, every county government entity is required to submit within a period of sixty (60) working days from the date of this advisory, an implementation plan for addressing the above challenges and adhering to the various provisions relating to the establishment and operationalisation of the internal audit function in the Public Finance Management Act, 2012, and related Regulations, and update the Commission on a quarterly basis on the progress made to implement the plan," EACC said.
