Several county governments, including Wajir, Siaya and Nairobi, continued processing billions of shillings in salaries through manual payroll systems despite a government directive requiring a transition to the Human Resource Information System (HRIS), a new report has revealed.
According to a report by Controller of Budget Margaret Nyakang’o, county governments processed at least Sh5.19 billion through manual payroll systems between July 2025 and March 2026, raising concerns over accountability and the potential misuse of public funds.
The report shows that 43 counties continued using manual payroll systems during the review period, with some payments being processed through vouchers, a practice that experts warn could create opportunities for fraud and payments to non-existent employees.
Most of the manual payroll payments involved salaries for thousands of casual workers and top-up allowances for security personnel.
Wajir County recorded the highest amount paid outside the approved digital system, processing Sh480 million through manual payroll. Siaya County followed with Sh401.65 million, while Nairobi County processed Sh311 million outside the Human Resource Information System.
Other counties that recorded significant manual payroll expenditures included Mandera, which processed Sh300.53 million, Tharaka Nithi at Sh261.18 million, Nakuru at Sh251.48 million and Kitui at Sh202 million.
The report indicates that thousands of county employees continued receiving salaries outside the Human Resource Information System, despite an April 2024 directive requiring all counties to migrate their payroll systems to the digital platform by June 2025.
Controller of Budget Margaret Nyakang’o warned that continued reliance on manual payroll systems poses serious risks to public finances.
“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),” said Nyakang’o.
In Siaya County, the administration of Governor James Orengo processed salaries for 1,811 casual workers through the manual payroll system, accounting for the county’s total manual payroll expenditure of Sh401.65 million.
Migori County, under Governor Ochilo Ayacko, paid 729 casual workers through the manual payroll system, while Marsabit County recorded 717 casual employees receiving salaries outside the digital platform.
Mandera County reported that 581 casual workers received Sh83.5 million through manual payroll during the reporting period. The county also spent Sh31 million on top-up allowances for security personnel.
Nakuru County, led by Governor Susan Kihika, continued paying 596 casual workers through manual payroll, while Busia County processed Sh82.4 million for 440 casual workers.
Busia Governor Paul Otuoma’s administration attributed the use of manual payroll to intermittent internet connectivity challenges and missing documentation from affected staff members.
The report further indicates that Lamu County processed Sh129.4 million through manual payroll, including Sh81.46 million paid to 534 casual workers.
Meru County processed Sh229 million outside the digital system, covering salaries for casual workers and top-up allowances for security personnel. Mombasa County, under Governor Abdulswamad Nassir, paid Sh207.94 million through manual payroll.
Kiambu County processed Sh136.13 million outside the Human Resource Information System, including Sh55.7 million paid to 4,220 casual workers. The county also spent Sh13.3 million on top-up allowances for 346 security personnel.
Kilifi County processed Sh84.17 million through manual payroll, including payments to casual staff and top-up allowances for national government security personnel deployed to the county.
Garissa County paid Sh12.27 million to 508 casual workers through manual payroll and spent an additional Sh7.2 million on security personnel allowances outside the digital system.
Elgeyo Marakwet County processed Sh160 million through manual payroll, including salaries for 113 casual workers and security personnel allowances amounting to Sh13.57 million and Sh3.48 million.
The report noted that Narok, Trans Nzoia, Turkana and Uasin Gishu were the only counties that reported no manual payroll payments during the period under review.
