County governments paid at least Sh8.3 billion in salaries using manual payrolls, avoiding approved digital systems implemented years ago in a move aimed at curbing fraud.
A new report by the Controller of Budget, Margaret Nyakang’o, has revealed that some counties paid staff using vouchers, a move prone to abuse through possible payment of ghost workers.
The manual payrolls were mostly used to pay casual staff and process top-up allowances to security personnel.
Nakuru, Wajir, Nairobi, Siaya and Mandera Counties led in the breaches flagged in Ms Nyakang'o's report, which covers 12 months to June 30, 2026.
Others are Meru, Elgeyo Marakwet, Kitui, Busia and Lamu.
According to the report, thousands of county employees are still deliberately paid salaries outside the Human Resource Information System (HRIS).
In April 2024, a directive was issued requiring counties to migrate payroll processing to the HRIS by June 2025.
On the flip side, Narok and Trans Nzoia Counties reported no manual payments.
“Manual payroll is prone to abuse and may result in the loss of public funds. The highest manual payroll shares were reported by Nakuru, Wajir, Nairobi, Siaya and Mandera,” said Dr Nyakang’o.
Controller of Budget Margaret Nyakango,
Photo credit: File | Nation Media Group
For instance, Governor Susan Kihika's Nakuru County processed Sh1.86 billion through manual payrolls, accounting for 21.8 per cent of the total personnel emoluments cost.
The manual payroll comprised salaries for 18 staff not onboarded into the HRIS, salaries for 596 casual staff, top-up allowances for security personnel, gratuity remittances to pension schemes for staff on contract, and pension contributions.
Governor Ahmed Abdullahi's office processed Sh755.35 million through manual payrolls, accounting for 14 per cent of the total personnel emoluments cost.
The justification for the continued use of manual payrolls was the delay in constituting the County Public Service Board and assigning payroll numbers.
Governor Johnson Sakaja's Nairobi County processed Sh496.07 million through manual payrolls in salaries for casual staff, top-up allowance for security officers, among others
Governor James Orengo-led Siaya County processed Sh401.65 million through manual payrolls, accounting for nine per cent of the total personnel emoluments cost.
The manual payroll comprised salaries for 477 staff not onboarded into the HRIS, salaries for 1,811 casual staff and top-up allowances for 11 security personnel.
Mandera County paid manually Sh362.41 million in salaries for 520 staff not onboarded into the HRIS, salaries for 581 casual staff, top-up allowances for security personnel, gratuity remittances to pension schemes for staff on contract and pension contributions.
Meru County processed Sh356.61 million through manual payrolls, accounting for seven per cent of the total personnel emoluments cost.
The manual payroll comprised salaries for 220 ward office employees, top-up allowances for security personnel, gratuity remittances to pension schemes for staff on contract, as well as pension contributions.
Elgeyo Marakwet spent Sh264.11 million manually to pay the salaries of officers employed on a casual basis.
The manual payroll comprised salaries for casual staff, top-up allowances for security personnel, gratuity remittances to pension schemes for contract staff as well as pension contributions.
Kitui County Governor Julius Malombe at Tseikuru Primary School in Kitui County on May 2, 2026.
Photo credit: Bonface Bogita | Nation Media Group
Governor Paul Otuoma's Busia County processed Sh230.93 million in salaries for 440 casual staff, gratuity remittances to pension schemes for staff on contract, and community health volunteers.
Lamu County processed Sh236.78 million through manual payrolls, accounting for 12 per cent of the total personnel emoluments cost.
The manual payroll included salaries for casual staff, top-up allowances for security personnel, and gratuity remittances to pension schemes for contract staff, as well as pension contributions for staff on contract.
Garissa County processed Sh231.53 million manually, comprising salaries for 547 staff not onboarded into the human resource information system, salaries for 521 casual staff, top-up allowances for 98 security personnel, and gratuity remittances to pension schemes for staff on contract.
Kajiado County spent Sh105.21 million through manual payroll for 307 casual staff, 123 partisan staff, and 15 interns.
Kericho County processed Sh202.3 million through manual payrolls for casuals and contract staff without payroll numbers.
Kiambu County spent Sh207.73 million manually through manual payroll relating to salaries for 4,220 casuals who had not been onboarded into the HRIS.
Kirinyaga County processed Sh98.57 million manually to pay mostly community health promoters and casual staff not integrated into the HRIS since January 2026.
Governor Gideon Mung'aro's Kilifi County processed Sh31.74 million manually to pay staff seconded from the national police service and could not be onboarded to the HRIS.
Kilifi Governor Gideon Mung'aro.
For Kisii County, Sh210.80 million was processed through manual payrolls.
Laikipia County paid Sh162.57 million manually, comprising salaries for 14 staff not onboarded into the HRIS, salaries for 85 casual staff, and top-up allowances for security personnel, and gratuity remittances.
Governor Wavinya Ndeti's Machakos County paid out Sh131.26 million manually, comprising salaries for staff not onboarded into the HRIS, salaries for 179 casual staff, gratuities for 18 contract staff, 60 MCAs’ mileage reimbursements, 60 ward staff service and salary advances for 15 staff and MCAs.
Governor Abdulswamad Nassir's Mombasa County processed Sh241.26 million through manual payrolls, comprising gratuity remittances to pension schemes for staff on contract.
Nandi County paid out Sh184.18 million manually in salaries for 211 staff not onboarded into the HRIS, salaries for 686 casual staff, and 21 top-up allowances for security personnel, and gratuity remittances to pension.
Taita Taveta County processed Sh108.25 million through manual payrolls for ward staff employees employed on a temporary basis; hence, they could not be onboarded to HRIS.
Additionally, security allowances were primarily for national government employees seconded to the county government.
At the heart of the payroll loophole is the payment of salaries to thousands of casual staff and top-up allowances to security personnel by county governments.
“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.
Tana River County processed Sh132.41 million manually, with the manual payroll comprising salaries for staff not on the HRIS, and for community health promoters.
Tharaka Nithi processed Sh157.16 million through manual payrolls, with the justification for the continued use of manual payrolls being that certain types of engagements are not long-term.
Turkana County paid out Sh141.30 million through manual payrolls, comprising deductions, gratuity remittances to pension schemes for staff on contract, and pension contributions.
Homa Bay County processed Sh89.73 million manually, comprising gratuity remittances to pension schemes for staff on contract.
Marsabit County processed Sh79.22 million manually in payment of casual staff and security officers engaged on a short-term basis.
Some Sh70.6 million was processed manually in salaries for 44 employees of Nyamira Water and Sanitation Company not onboarded into the HRIS, salaries for 25 casual staff, and stipends for community health promoters.
Uasin Gishu County paid out Sh42.99 million manually, comprising salaries for 169 staff not onboarded into the HRIS.
Vihiga County processed Sh59.92 million through manual payrolls in stipend payments to the community health volunteers and top-up allowances for the security officers.
Makueni County processed Sh35.85 million through manual payrolls in salaries for casual staff, top-up allowances for security personnel, gratuity remittances to pension schemes for staff on contract.
Baringo County paid Sh34.87 million through manual payroll in salaries to 205 casual staff, security personnel and gratuity remittances to pension schemes for staff on contract.
For Bungoma County , Sh80.55 million was processed through manual payrolls.
Kwale County paid Sh19 million manually in salaries for 90 assembly casual staff not onboarded into the HRIS.
Governor Abdi Guyo's Isiolo processed Sh4.32 million manually in top-up allowances for police officers deployed to the County Assembly.
