Auditor General Nancy Gathungu has revealed that nearly half of Kenya’s counties paid a total of Sh3.4 billion in salaries manually, bypassing the Integrated Payroll and Personnel Data (IPPD) system designed to control payroll and human resource management in the public sector.

This unauthorized practice violates the National Treasury Circular No.13/2019, which mandates that all personnel payments go through IPPD.

Among the 47 counties, Machakos and Nairobi led in manual payments, disbursing Sh487 million and Sh463.4 million, respectively.

Other counties with large sums paid manually include Garissa (Sh377.7 million), Marsabit (Sh288.6 million), Samburu (Sh319.6 million), and Nandi (Sh296.9 million). Counties like Nyeri, Kisumu, Mandera, and Laikipia also made sizeable manual salary payments. Smaller amounts were recorded in Nyandarua, Narok, and Nakuru among others.

The report further flagged six counties for retaining 302 employees who have exceeded the mandatory retirement age of 60 years, or 65 years for People with Disabilities (PWDs). Mombasa tops the list with 96 such workers, followed by Nakuru (77), Bungoma (79), Nandi (27), Migori (17), and Lamu (4).

“This failure to enforce retirement policies inflates the wage bill and limits employment opportunities. It may also point to a lack of succession planning within the counties,” the Auditor General’s report notes.

The report also uncovers irregularities in recruitment, promotions, payroll management, and staff confirmations. In Kisii, top candidates in interviews were overlooked, raising questions on fairness and transparency.

Mombasa promoted 16 employees without conducting performance appraisals, while Kisumu saw workers advance over two job groups within a year without clear justification. Nandi promoted staff despite unresolved disciplinary or integrity issues, undermining trust in the human resource system.

Delays in confirming staff to permanent roles are widespread. Nyamira had 1,779 employees on probation beyond six months, Bungoma 672, and Migori 1,126, depriving these workers of full employment rights and benefits.

Shared bank accounts for salary payments were also flagged as a risk. Bomet County’s salaries were deposited into such accounts, increasing the chance of fraud.

In Siaya, 20 employees shared the same bank account, while Narok hired 110 staff without proper human resource planning or clear justification for their roles.

The Auditor General’s findings highlight serious governance and financial risks facing counties, urging urgent reforms to restore compliance, accountability, and efficiency in public sector payroll and HR management.