County governments processed billions of shillings in staff payments through manual payrolls in the year to June 30, 2026, with some administrations continuing to pay workers outside the official digital system despite a directive to complete the transition.
At least Sh8.3 billion was paid through manual payrolls, according to a report by Controller of Budget Margaret Nyakang'o. The report 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, including casual employees, staff awaiting payroll numbers, security officers receiving top-up allowances, community health workers, gratuities and pension contributions.
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. However, 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.
"Manual payroll is prone to abuse and may result in the loss of public funds. The counties with the highest shares of manual payroll were Nakuru, Wajir, Nairobi, Siaya and Mandera," said Dr Nyakang'o.
Nakuru had the largest manual payroll bill, with Sh1.86 billion processed outside the HRIS. The amount represented 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, among other payments.
In Siaya, Sh401.65 million was paid through manual payrolls, accounting for nine per cent of total personnel emoluments. The payments covered 477 employees who had not been onboarded onto the HRIS, 1,811 casual workers and top-up allowances for 11 security personnel.
Mandera processed Sh362.41 million manually. This covered salaries for 520 workers who were not enrolled in the HRIS, 581 casual workers and security personnel. It also included gratuity remittances to pension schemes for contracted staff and pension contributions.
Meru recorded Sh356.61 million in manual payroll payments, equal to seven per cent of its personnel emoluments. The county used the money to pay 220 ward office employees, security personnel top-up allowances, gratuity remittances for contract staff and pension contributions.
Elgeyo Marakwet processed Sh264.11 million manually, mainly for casual workers.
Kitui paid Sh259.36 million through manual payrolls. The payments covered casual staff, top-up allowances for security personnel, gratuity remittances to pension schemes for contract staff and pension contributions.
Busia processed Sh230.93 million manually for 440 casual workers, gratuity remittances to pension schemes for contract staff and community health volunteers.
Lamu recorded Sh236.78 million in manual payroll payments, equivalent to 12 per cent of its total personnel emoluments. The payments included casual staff salaries, security personnel top-up allowances, gratuity remittances to pension schemes for contract staff and pension contributions for contracted employees.
Garissa processed Sh231.53 million outside the HRIS. This comprised salaries for 547 employees who had not been onboarded into the system, payments to 521 casual workers, top-up allowances for 98 security personnel and gratuity remittances to pension schemes for contract staff.
Kajiado paid Sh105.21 million manually for 307 casual workers, 123 partisan staff and 15 interns.
Kakamega processed Sh62.7 million through manual payrolls.
Kericho paid Sh202.3 million manually to casual and contract workers who did not have payroll numbers. The amount included salaries for 185 employees who had not yet been onboarded into the HRIS.
Kiambu processed Sh207.73 million manually for 4,220 casual workers who had not been integrated into the HRIS.
Kirinyaga paid Sh98.57 million manually to community health promoters and casual workers who had not been added to the HRIS since January 2026. The payments covered 960 casual employees and stipends for 854 community health promoters.
In Kilifi, Governor Gideon Mung'aro's administration processed Sh31.74 million manually to pay staff seconded from the national police service who could not be onboarded into the HRIS.
Kisii processed Sh210.80 million through manual payrolls, while Laikipia paid Sh162.57 million manually. The Laikipia payments comprised salaries for 14 employees not onboarded into the HRIS, 85 casual workers, security personnel top-up allowances and gratuity remittances.
Machakos processed Sh131.26 million outside the digital payroll. The amount covered salaries for workers not onboarded into the HRIS, 179 casual workers, gratuities for 18 contract workers, mileage reimbursements for 60 MCAs, service and salary advances for 60 ward workers, as well as salary advances for 15 workers and MCAs.
Mombasa processed Sh241.26 million through manual payroll, with the payments comprising gratuity remittances to pension schemes for contract workers.
Murang'a paid Sh130.09 million manually, while Nandi processed Sh184.18 million outside the HRIS. Nandi's payments included salaries for 211 workers who had not been onboarded, salaries for 686 casual workers, top-up allowances for 21 security personnel, gratuity remittances to pension schemes for contract workers and pension contributions.
Taita Taveta processed Sh108.25 million through manual payrolls for temporary ward employees who could not be onboarded into the HRIS. The county also reported that security allowances were mainly paid to national government employees seconded to the county administration.
Tana River processed Sh132.41 million manually, covering salaries for workers outside the HRIS and payments to community health promoters.
Tharaka Nithi paid Sh157.16 million through manual payrolls, with the county saying some of the engagements were temporary and not long-term.
Turkana processed Sh141.30 million manually. The payments comprised deductions, gratuity remittances to pension schemes for contract staff and pension contributions.
Homa Bay paid Sh89.73 million through manual payroll, mainly for gratuity remittances to pension schemes for contract workers.
Marsabit processed Sh79.22 million manually to pay casual workers and security officers hired on a short-term basis.
The Controller of Budget said counties cited several operational challenges and payment categories as reasons for retaining manual payrolls.
"The main reasons cited for manual payroll were delayed issuance of personal or payroll numbers, incomplete HRIS-Ke onboarding, temporary casual staff, gratuity and statutory payments, security top-up allowances, connectivity challenges, and missing staff documentation," said Dr Nyakang'o.
Narok and Trans Nzoia, however, reported no manual payroll payments during the period covered by the report.