County governments in Kenya processed Sh8.3 billion in staff payments through manual payrolls in the year to June 30, 2026. A report by Controller of Budget Margaret Nyakang'o raises concerns over payroll controls, noting that payments made outside approved digital systems can create room for abuse, including the possible inclusion of ghost workers. The manual payments covered a wide range of workers and expenses.
Nakuru, Wajir, Nairobi, Siaya, and Mandera recorded the largest shares of manual payroll payments among the counties flagged in the report. Meru, Elgeyo Marakwet, Kitui, Busia, and Lamu were also among the counties that continued to process substantial payments outside the Human Resources Information System (HRIS). An April 2024 directive required county governments to shift payroll processing to the HRIS by June 2025.
Nakuru had the largest manual payroll bill, with Sh1.86 billion processed outside the HRIS, representing 21.8 per cent of the county's total personnel emoluments. The payments included salaries for 18 employees who had not been entered into the HRIS, 596 casual workers, security personnel top-up allowances, gratuity remittances to pension schemes for contracted staff, and pension contributions.
Wajir recorded Sh755.35 million in manual payroll payments, representing 14 per cent of its personnel emoluments. The county explained that the practice was linked to delays in establishing the County Public Service Board and issuing payroll numbers. Nairobi processed Sh496.07 million manually, with the money going towards casual workers' salaries and top-up allowances for security officers.
Siaya, Mandera, Meru, Elgeyo Marakwet, and Kitui also recorded significant manual payroll payments. In Siaya, Sh401.65 million was paid through manual payrolls, accounting for nine per cent of total personnel emoluments. Mandera processed Sh362.41 million manually, covering salaries for 520 workers who were not enrolled in the HRIS, 581 casual workers, and security personnel.
Other counties, including Busia, Lamu, Garissa, Kajiado, Kakamega, Kericho, Kiambu, Kirinyaga, Kilifi, Kisii, Laikipia, and Machakos, also made manual payroll payments. The Controller of Budget's review for the 12 months ending June 30, 2026, found that thousands of workers were still being paid outside the system.
The report's findings highlight the need for county governments to fully transition to the HRIS to ensure better payroll controls and reduce the risk of abuse. Key counties with large manual payroll payments include Nakuru (Sh1.86 billion), Wajir (Sh755.35 million), and Nairobi (Sh496.07 million).
Key points
- Sh8.3 billion was paid through manual payrolls by county governments.
- Nakuru, Wajir, and Nairobi recorded the largest shares of manual payroll payments.
- The manual payroll payments covered a wide range of workers and expenses.
