NAIROBI, Kenya – At least 40 county governments processed more than Sh1.52 billion in staff salaries outside the mandatory Human Resource Information System (HRIS) in just three months, raising fresh concerns over payroll fraud, inflated wage bills and possible loss of public funds.
According to the Controller of Budget’s first quarter review for the financial year ending June 30, 2026, thousands of county employees remain off the electronic payroll, with governors continuing to rely on manual systems despite repeated warnings from oversight bodies.
Controller of Budget Margaret Nyakang’o said the widespread use of manual payrolls exposes counties to abuse and weakens accountability in public spending.
“Manual payroll is prone to abuse and may result in the loss of public funds,” Dr Nyakang’o noted in the report.
Nairobi, Nyeri, Siaya, Elgeyo Marakwet and Nakuru counties recorded the highest manual payments during the quarter, collectively accounting for hundreds of millions of shillings paid outside the HRIS.
Nyeri County alone processed Sh109.65 million manually, covering 152 staff not onboarded to the system, 57 casual workers, security top-up allowances and pension contributions.
Nairobi City Hall paid Sh109.61 million, largely for ward staff, casual workers, community health workers and funeral home staff.
In Siaya, the county disbursed Sh105 million manually, including Sh54.7 million for 1,021 staff not captured in the HRIS and Sh55.2 million paid to nearly 9,000 casual employees.
Nakuru County followed closely with Sh97.63 million, while Elgeyo Marakwet processed Sh92.75 million outside the system.
Other counties that relied heavily on manual payroll included Mombasa (Sh77.15 million), Lamu (Sh70.85 million), Mandera (Sh50.49 million), Kitui (Sh41.15 million), Nandi (Sh40.13 million), Meru (Sh35.34 million) and Machakos (Sh31 million).
Several counties — among them Busia, Turkana, Garissa, Kiambu, Kericho, Kilifi and Kirinyaga — also processed millions manually, often citing payments for casual staff, security allowances and pension contributions.
At the lower end, counties such as Kakamega, Nyandarua, Bomet, Kajiado, Homa Bay, Embu, Samburu, Tana River, Vihiga, Kisii, Makueni, Isiolo, Tharaka Nithi, Kisumu, Bungoma, Kwale, Narok and Marsabit recorded manual payroll payments ranging from Sh4 million to below Sh500,000.
Only a handful of counties — including Baringo, Migori, Nyamira, Trans Nzoia, Uasin Gishu and West Pokot — fully complied with the HRIS requirement during the quarter.
Wajir County did not pay any staff salaries during the period after delays in budget approval, despite Sh44.48 million having been authorised for payroll from its county revenue fund.
The latest findings mirror a long-running trend. In the first quarter of the 2023–2024 financial year, counties spent more than Sh3 billion outside the HRIS, while manual payroll payments hit Sh15 billion in the 2021–2022 period.
Auditor-General Nancy Gathungu has repeatedly warned that bypassing the electronic payroll system encourages ghost workers, inflated wage bills and outright fraud.
Counties have often blamed delays in issuing personal numbers to employees for the continued use of manual payments.
The Controller of Budget says the failure to fully implement the HRIS remains a major governance gap, leaving billions of shillings in public funds vulnerable to misuse.
