Makueni Governor Mutula Kilonzo Jnr. File Photo. 
By Andrew Mbuva
A special audit by the Office of the Auditor-General has exposed widespread weaknesses and irregularities in payroll and human resource management at the Makueni County Executive, raising serious concerns over financial discipline, accountability and compliance with the law .
The audit, which covered three financial years from 2021/2022 to 2023/2024, found that the county persistently breached the legal requirement that employee compensation should not exceed 35 per cent of total revenue. While the law seeks to ensure counties retain enough funds for development and service delivery, Makueni’s actual personnel costs surpassed the threshold in all three years under review, at times reaching nearly half of total revenue .
Auditors noted that this trend has strained the county’s finances, limiting resources available for critical development projects and essential services. They also pointed to weak oversight by the County Assembly in enforcing fiscal responsibility principles.
The report further revealed serious inconsistencies between payroll systems and approved budgets. Vote heads configured in the Integrated Payroll and Personnel Database (IPPD) and the newer Human Resource Information System–Kenya (HRIS-Ke) did not align with those in the approved budget or the Integrated Financial Management Information System (IFMIS). As a result, salaries were charged to incorrect budget lines, undermining accurate financial reporting and increasing the risk of misuse of public funds .
In recruitment, the county hired 490 employees over the three years without approved annual recruitment plans. Auditors said the absence of structured human resource planning exposed the county to overstaffing, understaffing and hiring that may not align with service delivery priorities. Additionally, some job designations captured in the payroll system were not included in the approved staff establishment, raising the risk of unauthorised appointments and irregular salary payments .
Data integrity issues also featured prominently. The audit found that birth dates for 372 employees recorded in the payroll system differed from official birth certificates, contrary to Public Service Commission guidelines. This anomaly could result in staff serving beyond retirement age or being retired prematurely, as well as errors in pension and retirement benefit calculations.
More troubling were cases of possible “double dipping”. Ten employees were found to be drawing salaries simultaneously from Makueni County and other government entities, earning a combined Sh9.67 million during the period under review. Auditors questioned the legality and ethics of such dual employment, noting it violated principles of prudent financial management .
The report also highlighted failures by Chief Officers to fully account for staff in their departments. While some employees appeared on departmental lists but not on the central payroll, others were paid through the payroll system yet were unknown to departmental heads. In one year alone, 173 such employees received over Sh15 million in salaries, raising concerns over the authenticity of parts of the payroll .
On statutory compliance, the county was cited for delayed remittance of National Social Security Fund (NSSF) and National Health Insurance Fund (NHIF) deductions, leading to penalties and interest. In the 2021/2022 financial year, Makueni incurred Sh3.25 million in avoidable interest and penalties—classified by the Auditor-General as nugatory expenditure.
The audit further found that the county was in breach of ethnic diversity laws. As at June 2024, 93 per cent of staff were drawn from one dominant ethnic community, far exceeding the one-third limit set by law. New recruitment during the period averaged 92 per cent from the same community, exposing the county to potential legal action and undermining inclusivity principles .
Challenges also emerged during the transition from IPPD to HRIS-Ke in late 2024. Auditors identified cases of overpayments and underpayments of salaries and allowances following the migration, as well as employees who were either omitted or irregularly introduced into the new system. These errors were attributed to weak data validation and inadequate reconciliation controls.
In its conclusion, the Auditor-General stated that the payroll problems had persisted over time, pointing to ineffective risk management and a weak internal audit function within the county. The report recommends strict enforcement of the wage bill cap, alignment of payroll systems with approved budgets and staff establishments, recovery of irregular payments, and disciplinary action against responsible officers.
“The weaknesses identified expose the county to financial loss, legal risk and reputational damage,” the report warns, urging urgent reforms to restore integrity and accountability in Makueni’s payroll management .
