At least Sh5.19 billion in county salary payments was processed outside the government's approved digital payroll platform over a nine-month period, with Wajir, Siaya and Nairobi emerging as the biggest users of manual payroll despite a directive requiring all counties to fully migrate to the Human Resource Information System (HRIS).
The latest report by Controller of Budget Margaret Nyakang’o reveals that 43 counties continued relying on manual payroll between July 2025 and March 2026, raising concerns over accountability and increasing the risk of irregular salary payments.
According to the report, counties mainly used the manual system to pay casual workers and provide top-up allowances to security personnel.
Wajir recorded the highest amount processed outside the digital platform after paying Sh480 million through manual payroll. Siaya followed with Sh401.65 million, while Nairobi processed Sh311 million outside HRIS.
Mandera paid Sh300.53 million manually during the review period, while Tharaka Nithi recorded Sh261.18 million. Nakuru followed with Sh251.48 million and Kitui with Sh202 million.
The report shows that many county governments were still paying employees outside the official payroll platform even after an April 2024 directive ordered all counties to migrate to HRIS by June 2025.
Nyakang’o warned that the continued use of manual payroll systems exposes public funds to unnecessary risks.
“Manual payroll is prone to abuse and may result in the loss of public funds. Counties with the highest shares of manual payroll were Siaya (13.8 per cent), Wajir (12.7 per cent), Tharaka Nithi (12.5 per cent) and Lamu (10.1 per cent),” Nyakang’o said.
In Siaya, salaries for 1,811 casual workers were processed through manual payroll, accounting for expenditure amounting to Sh401.65 million.
Migori reported 729 casual workers paid outside the digital system, while Marsabit used manual payroll to pay 717 casual employees.
Mandera recorded 581 casual workers who received Sh83.5 million through manual payroll. The county also spent Sh31 million on top-up allowances for security personnel.
In Nakuru, salaries for 596 casual workers continued to be processed manually. Busia paid Sh82.4 million through manual payroll covering 440 casual workers.
Busia attributed the use of the manual system to unstable internet connectivity and incomplete staff records.
Lamu processed Sh129.40 million through manual payroll, including Sh81.46 million paid to 534 casual workers.
Meru reported Sh229 million in manual payroll payments covering casual workers and security personnel allowances, while Mombasa processed Sh207.94 million outside the digital platform.
Kiambu paid Sh136.13 million through manual payroll, including Sh55.7 million for 4,220 casual workers. The county also spent Sh13.3 million on top-up allowances for 346 security personnel.
Kilifi processed Sh84.17 million through manual payroll for casual workers and national government security officers temporarily assigned to the county.
Garissa paid Sh12.27 million to 508 casual workers outside HRIS and spent a further Sh7.2 million on security personnel allowances through the manual system.
Elgeyo Marakwet recorded Sh160 million in manual payroll payments. The amount included salaries for 113 casual workers and security personnel allowances amounting to Sh13.57 million and Sh3.48 million respectively.
“The 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,” Nyakang’o said.
The report further shows that Narok, Trans Nzoia, Turkana and Uasin Gishu were the only counties that did not process any salaries through manual payroll during the period under review.