How 40 counties spent Sh1.52bn outside approved payroll

By Newsflash Writer

Forty county governments paid at least Sh1.52 billion in staff salaries through manual payrolls within just three months, sidestepping the approved Human Resource Information System (HRIS), a new report has disclosed.

The hard-hitting report by Controller of Budget (CoB) Margaret Nyakang’o reveals a worrying trend in which devolved units deliberately fail to onboard staff onto the HRIS, opening the door to manual salary processing. The County Governments’ Budget Implementation Review Report for the first quarter of the financial year ending June 30, 2026, singled out Nairobi, Nyeri, Siaya, Elgeyo Marakwet and Nakuru as the worst offenders. According to the report, thousands of county workers remain outside the system, exposing governments to potential losses through ghost workers. The situation is compounded by payments to large numbers of casual staff and top-up allowances for security personnel.

“Manual payroll is prone to abuse and may result in the loss of public funds,” Dr Nyakang’o warned. Only six counties — Baringo, Migori, Nyamira, Trans Nzoia, Uasin Gishu and West Pokot — fully paid staff salaries through HRIS. Wajir County, however, reported no staff compensation during the period, blaming delays in the approval of budget estimates and the Appropriation Act 2025, despite CoB authorising a Sh44.48 million withdrawal from its revenue fund exclusively for personnel costs.

Billions paid outside approved systems

The review reiterates that Nairobi, Nyeri, Siaya, Elgeyo Marakwet and Nakuru were the biggest culprits during the quarter under review. Thousands of workers remain outside HRIS, increasing the risk of financial leakages through fictitious employees. Salaries for casual staff and security top-ups continue to fuel the practice. Over the years, the CoB has repeatedly flagged counties for processing billions of shillings manually, linking the trend to bloated wage bills and ghost workers. In the first quarter of the year ending June 30, 2024, counties paid over Sh3 billion through manual payrolls, while in the financial year ended June 30, 2022, payments outside approved systems hit a staggering Sh15 billion.

Auditor-General Nancy Gathungu has also issued damning findings on the issue, repeatedly warning that bypassing authorised payroll systems forms part of elaborate fraud schemes that have drained billions of shillings from public coffers. The law does not sanction manual payrolls, which are closely associated with runaway wage bills. Nonetheless, counties often cite the lack of personal numbers for staff as justification for non-compliance.

Nyeri County under Governor Mutahi Kahiga processed Sh109.65 million manually, covering salaries for 152 staff not onboarded to HRIS, 57 casual workers, security top-up allowances, gratuity for contract staff and pension contributions.

Counties, figures and justifications

At City Hall, Nairobi processed Sh109.61 million manually, including Sh23.7 million for ward staff outside HRIS and Sh85.89 million for City Funeral Home, Lang’ata Cemetery, mobility casuals and community health workers. Siaya County, led by Governor James Orengo, processed Sh105 million, paying Sh54.7 million to 1,021 non-onboarded staff, Sh55.2 million to 8,990 casuals and Sh1 million in security top-ups, alongside pension-related payments. Nakuru County paid Sh97.63 million manually, including Sh56.5 million to 756 casual staff.

Elgeyo Marakwet processed Sh92.75 million — 13 per cent of its wage bill — manually due to 917 staff yet to be onboarded. Laikipia paid Sh20.48 million to 1,180 staff outside HRIS, while Mombasa processed Sh77.15 million, with Sh57 million going to executive and assembly staff. Lamu paid Sh70.85 million amid challenges with casuals and unregistered staff, while Busia processed Sh59.25 million covering non-onboarded staff, casuals and stipends for community health promoters.

Turkana spent Sh53.73 million outside the system, Garissa Sh57.36 million, Kiambu Sh56.52 million, Kericho Sh45.02 million, and Kilifi and Kirinyaga Sh32.76 million and Sh32.98 million respectively. Mandera paid Sh50.49 million, Kitui Sh41.15 million, Nandi Sh40.13 million and Meru Sh35.34 million. Machakos processed Sh31 million, Murang’a Sh28.61 million and Taita Taveta Sh26.74 million.

Kakamega paid Sh26.92 million, Nyandarua Sh25.33 million, Bomet Sh18.92 million, Kajiado Sh13.5 million, Homa Bay assembly Sh14.24 million, Embu Sh12.38 million and Samburu Sh12.09 million. Tana River paid Sh11.50 million, Vihiga Sh11.30 million, Kisii Sh10.61 million and Makueni Sh8.39 million. Isiolo paid Sh6.84 million, Tharaka Nithi Sh5.46 million and Kisumu Sh5.96 million. Bungoma processed Sh4.30 million, while Kwale paid Sh4 million. Narok (Sh104,179) and Marsabit (Sh241,000) reported the lowest manual payroll expenditures, each below Sh500,000.