At least 40 county governments paid more than Ksh1.52 billion in salaries through manual payroll systems in just three months, defying mandatory use of the Human Resource Information System (HRIS), a new Controller of Budget report shows.
The first-quarter review for the 2025/2026 financial year warns that thousands of county employees remain outside the electronic payroll, exposing public funds to abuse, irregular payments and potential loss.
Counties including Nairobi, Nyeri, Siaya, Nakuru and Elgeyo Marakwet recorded the highest manual payments. In contrast, Baringo, Migori, Nyamira, Trans Nzoia, Uasin Gishu and West Pokot fully complied with HRIS requirements.
Controller of Budget Margaret Nyakang’o cautioned that continued reliance on manual payroll undermines accountability and enables payroll fraud. The report notes that manual salary payments have persisted for years, with counties previously spending billions outside the approved system.
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