Wajir, Siaya and Nairobi were among the counties that processed the highest amounts of salaries through manual payroll despite a directive requiring all county governments to migrate to the Human Resource Information System, with a new report showing at least Sh5.19 billion was paid outside the digital platform.
The report by Controller of Budget Margaret Nyakang’o shows that 43 counties continued using manual payroll systems between July 2025 and March 2026, with some payments being made through vouchers, a practice that could expose public funds to abuse through possible payments to ghost workers.
The manual payroll payments mainly involved salaries for thousands of casual workers and top-up allowances for security personnel, according to the report.
Wajir County recorded the highest amount paid manually after processing Sh480 million outside the approved system. It was followed by Siaya County, which paid Sh401.65 million manually, and Nairobi County, which processed Sh311 million outside the Human Resource Information System.
Other counties that recorded high manual payroll payments included Mandera at Sh300.53 million, Tharaka Nithi at Sh261.18 million, Nakuru at Sh251.48 million and Kitui at Sh202 million.
The report stated that thousands of county employees continued receiving salaries outside the Human Resource Information System either deliberately or by default, despite an April 2024 directive requiring counties to move payroll processing to the digital system by June 2025.
Nyakang’o warned that continued reliance on manual payroll systems created risks for public funds.
“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, Governor James Orengo’s administration processed salaries outside the system for 1,811 casual workers. The county’s manual payroll expenditure stood at Sh401.65 million.
Migori County, under Governor Ochilo Ayacko, had 729 casual workers paid through the manual system, while Marsabit had 717 casual employees.
Mandera County reported 581 casual workers who 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, under Governor Susan Kihika, continued paying 596 casual workers manually, while Busia processed Sh82.4 million through manual payroll for 440 casual workers.
Governor Paul Otuoma’s administration said the use of manual payroll was caused by intermittent connectivity challenges and missing documentation from affected staff.
The report further shows that Lamu County processed Sh129.40 million through manual payroll, including Sh81.46 million paid as salaries for 534 casual workers.
Meru County processed Sh229 million manually, covering salaries for casual workers and top-up allowances for security personnel, while Mombasa County, under Governor Abdulswamad Nassir, paid Sh207.94 million through manual payroll.
Kiambu County processed Sh136.13 million outside the digital system, including Sh55.7 million in salaries for 4,220 casual workers. The county also paid Sh13.3 million in top-up allowances for 346 security personnel.
Kilifi County processed Sh84.17 million through manual payroll, including top-up allowances for national government security personnel temporarily seconded to the county and payments for casual staff.
Garissa County paid Sh12.27 million manually to 508 casual workers and spent another Sh7.2 million outside the system on security personnel top-up allowances.
Elgeyo Marakwet processed Sh160 million through manual payroll, including salaries for 113 casual workers and top-up allowances for security personnel 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 noted that Narok, Trans Nzoia, Turkana and Uasin Gishu were the only counties that reported no manual payroll payments during the period under review.
Comments
Sign in with Google to comment, reply, and like comments.
Continue with Google