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.
A new report by the Controller of Budget, Margaret Nyakang’o, has laid bare how counties manually spent at least Sh5.19 billion on salaries between July 2025 and March this year, circumventing approved digital payroll systems.
The damning report revealed that 43 devolved units used manual payrolls, with some even paying staff using vouchers, a move prone to abuse through the possible payment of ghost workers.
At the heart of the payroll loophole is the payment of salaries to thousands of casual staff and top-up allowances to security personnel.
Wajir, Mandera, Siaya, Tharaka Nithi, Nairobi, Nakuru, Kitui, Laikipia, Lamu and Migori were identified as the biggest culprits.
The Controller of Budget Margaret Nyakang'o.
According to the report, thousands of county employees are still, deliberately or by default, being paid salaries outside the Human Resource Information System (HRIS).
In April 2024, a directive required county entities to migrate payroll processing to the HRIS by June 2025.
On the flip side, Narok, Trans Nzoia, Turkana and Uasin Gishu 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 Siaya at 13.8 percent, Wajir at 12.7 percent, Tharaka Nithi at 12.5 percent and Lamu at 10.1 percent,” said Dr Nyakang’o.
For instance, Governor Ahmed Abdullahi’s Wajir County paid Sh480 million manually, Mandera Sh300.53 million, Nairobi Sh311 million, Tharaka Nithi Sh261.18 million, Nakuru Sh251.48 million and Kitui Sh202 million.
Governor James Orengo’s Siaya spent Sh401.65 million outside the system, paying salaries for 1,811 casual staff.
Following closely was Governor Ochilo Ayacko’s Migori administration, which has 729 casual staff, and Marsabit, with 717 such staff.
Mandera County has a total of 581 casual staff who were paid Sh83.5 million during the reporting period, while top-up allowances for security personnel amounted to Sh31 million.
Governor Susan Kihika’s Nakuru has 596 casual staff who are still paid manually, while Busia County has 440 such staff who were paid Sh82.4 million manually during the reporting period.
Governor Paul Otuoma’s administration said the continued use of manual payroll was due to intermittent connectivity and a lack of documentation from the affected staff.
The report indicated that Lamu County processed Sh129.40 million through manual payroll, comprising Sh81.46 million in salaries for 534 casual staff.
In Meru County, Sh229 million was processed manually, including salaries for casual staff and top-up allowances for security personnel, while Governor Abdulswamad Nassir’s Mombasa spent Sh207.94 million manually.
Mombasa Governor Abdulswamad Shariff Nassir when he appeared before the Senate County Public Accounts Committee at Bunge Tower in Nairobi on June 4, 2026.
Kiambu County processed Sh136.13 million through manual payrolls, with salaries for 4,220 casual staff amounting to Sh55.7 million and top-up allowances for 346 security personnel totalling Sh13.3 million.
Some Sh84.17 million was processed through manual payroll in Kilifi County, including top-up allowances for national government security personnel temporarily seconded to the county, as well as salaries for casual staff.
Garissa County has 508 casual staff who were paid Sh12.27 million manually, while another Sh7.2 million was spent outside the system on top-up allowances for security personnel.
Elgeyo Marakwet processed Sh160 million manually, comprising salaries for 113 casual staff and top-up allowances for security personnel amounting to Sh13.57 million and Sh3.48 million, respectively.
Nairobi processed Sh311.95 million through manual payrolls for salaries for casual staff, top-up allowances for security officers, among other payments.
In Nandi County, Sh111.04 million was processed through manual payrolls, while Nyamira County processed Sh44.52 million manually.
Tana River spent Sh125.11 million outside the system, citing delays in obtaining personal identification numbers for new staff and county assembly ward office staff employed on contract.
“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.
Machakos County paid Sh96.13 million outside the system, with salaries for 179 casual ward staff amounting to Sh42.3 million. Kericho processed Sh65 million manually, while Governor Joseph Ole Lenku’s Kajiado spent Sh87.49 million manually to pay salaries for 307 casual staff and top-up allowances for security personnel.
Murang’a County processed Sh123.63 million through manual payroll due to delays by the Directorate of Public Service Management in issuing staff with personal numbers for integration into the HRIS, as well as the county’s internship programme, whose interns are not integrated into the system.
Nyandarua County processed Sh97.37 million through manual payrolls for newly recruited staff who had yet to acquire personal numbers, payment of statutory contributions not directly populated in the HRIS, and payment of interns.
Nyeri County Governor Mutahi Kahiga when he appeared before the Senate County Public Investments Committee at Bunge Tower in Nairobi.
Governor Mutahi Kahiga’s Nyeri County processed Sh193 million manually, while Embu processed Sh37.36 million, Homa Bay Sh61.49 million, Kirinyaga Sh133.67 million, Kisii Sh14.79 million, Kisumu Sh32.89 million and Kwale County Assembly Sh14 million.
Vihiga County processed a paltry Sh7.31 million outside the HRIS, mainly for payments to community health workers who are not defined in the system, while West Pokot processed Sh8.78 million for salaries for casual staff and top-up allowances for security personnel.
Laikipia County processed Sh153.76 million through manual payroll without providing justification for the continued use of the system.
In Makueni County, Sh55.86 million was processed through manual payroll for salaries for casual staff, top-up allowances for security personnel and other payments, while Baringo County spent Sh10.80 million manually to pay salaries for 205 casual staff.
Taita Taveta processed Sh57.35 million manually, Bungoma Sh62.65 million, Samburu Sh12.49 million and Bomet Sh1.1 million.
In Isiolo and Kakamega counties, it was the county assemblies that paid staff through manual payrolls, with Isiolo County Assembly processing Sh51.30 million and Kakamega County Assembly processing Sh7.79 million manually.
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