NAIROBI, Kenya — Kenyan counties processed at least Sh8.3 billion in staff payments through manual payrolls in the year ended June 30, 2026, despite a government directive requiring devolved units to migrate payroll processing to the Human Resources Information System (HRIS).
Controller of Budget Margaret Nyakang’o said several counties continued using manual payrolls for casual workers, security allowances, gratuities and employees who had not been onboarded onto the digital system.
The migration to HRIS was expected to be completed by June 2025.
Nyakang’o warned that continued reliance on manual payrolls exposed public funds to potential abuse, including the risk of payments being made to non-existent workers.
“Manual payroll is prone to abuse and may result in the loss of public funds,” Nyakang’o said.
Nakuru Leads Manual Payroll Spending
Nakuru recorded the highest manual payroll expenditure, processing Sh1.86 billion, equivalent to 21.8 per cent of its personnel emoluments.
The payments included salaries for 18 staff who had not been entered into the HRIS, 596 casual workers, security top-up allowances, gratuities and pension contributions.
Nairobi followed with Sh496.07 million, mainly covering casual staff salaries, security allowances and other payments.
Siaya processed Sh401.65 million, equivalent to nine per cent of its personnel costs. The payments included 477 staff who had not been onboarded onto HRIS, 1,811 casual workers and 11 security personnel.
Mandera processed Sh362.41 million for 520 staff outside the HRIS, 581 casual workers, security personnel, gratuities and pension contributions.
More Counties Remain Outside Digital Payroll
Meru processed Sh356.61 million, equivalent to seven per cent of personnel costs, including payments to 220 ward office workers, security allowances, gratuities and pension contributions.
Elgeyo Marakwet spent Sh264.11 million on casual staff, while Kitui processed Sh259.36 million for casual workers, security allowances, gratuities and pension contributions.
Lamu spent Sh236.78 million, representing 12 per cent of its personnel costs, while Busia processed Sh230.93 million for 440 casual workers, gratuities and community health volunteers.
Garissa processed Sh231.53 million, covering 547 staff not onboarded onto HRIS, 521 casual workers, 98 security personnel and gratuities.
Kisii recorded Sh210.80 million, while Kiambu processed Sh207.73 million for 4,220 casual workers.
Kericho spent Sh202.30 million on casual and contract workers without payroll numbers, including 185 employees who had not been onboarded onto HRIS.
Nandi processed Sh184.18 million for 211 staff outside the system, 686 casual workers, security allowances, gratuities and pension contributions.
Laikipia recorded Sh162.57 million, while Tharaka Nithi processed Sh157.16 million, citing short-term engagements.
Turkana spent Sh141.30 million on deductions, gratuities and pension contributions, while Machakos processed Sh131.26 million for staff outside HRIS, 179 casual workers, 18 contract staff, mileage for 60 MCAs and salary or service advances.
Murang’a processed Sh130.09 million, while Taita Taveta recorded Sh108.25 million for temporary ward staff and security allowances.
Kajiado spent Sh105.21 million on 307 casual staff, 123 partisan staff and 15 interns.
Kirinyaga processed Sh98.57 million for 960 casual workers and stipends for 854 community health promoters.
Homa Bay recorded Sh89.73 million, mainly in gratuities, while Marsabit processed Sh79.22 million for casual workers and security officers.
Kakamega recorded Sh62.70 million, while Kilifi processed Sh31.74 million for national police officers seconded to the county who could not be onboarded onto HRIS.
Manual Payments Driven By Multiple Challenges
Mombasa processed Sh241.26 million, mainly for gratuity remittances to pension schemes for contract staff.
Tana River recorded Sh132.41 million for staff outside HRIS and community health promoters.
The Controller of Budget said counties cited several reasons for continuing with manual payrolls.
These included delays in issuing personal or payroll numbers, incomplete HRIS onboarding, temporary employment of casual workers, gratuity and statutory payments, security top-up allowances, connectivity problems and missing staff documentation.
Despite the widespread use of manual payrolls, Narok and Trans Nzoia reported no manual payroll payments during the period under review.
The findings have renewed concerns over payroll controls in county governments and the need to ensure all eligible employees are captured in the digital system to strengthen accountability and reduce the risk of loss of public funds.
