3 Critical Treasury Directives Reshaping April County Payrolls Nationwide
National Treasury PS Chris Kiptoo.
The National Treasury has officially directed all counties to transition to a new integrated payroll system starting this April.
The government move is a decisive move aimed to eliminate the persistent issue of ghost workers and ensure the seamless remittance of statutory deductions across devolved units.
By synchronizing the Human Resource Information System (HRIS-Kenya) with the Integrated Financial Management Information System (IFMIS), the government is moving to secure public funds and bolster fiscal accountability.
3. Eliminating the Ghost Worker Epidemic
County payrolls have been plagued by the presence of “ghost workers” for many years. Recent estimates indicate that nearly Sh33.5 billion was lost to non-existent staff in the 2024/25 fiscal year alone.
Counties like Nairobi, Nandi, and Samburu reported significant percentages of untraceable personnel during verification audits. By forcing all staff onto the integrated module, the Treasury ensures that every salary payment is tied to a verified, active employee identity.
According to experts, the system makes it nearly impossible for manual, non-integrated payrolls to hide phantom employees, effectively closing a major loophole that has drained billions from the public purse.
2. Automating Statutory Deductions for Seamless Compliance
Beyond identifying ghost workers, the integrated system simplifies the complex web of statutory obligations.
Previously, many state agencies struggled with the non-remittance of mandatory contributions, leading to systemic inefficiencies. Under the new directive, statutory deductions—including SHA, NSSF, PAYE, and Pension—are now automatically “twinned” with net salary payments.
Once a salary is processed, the system immediately forwards these funds to the respective government entities.
1. Leveraging Controller of Budget Oversight
Compliance is no longer optional for county governments as the Treasury has instituted a hard enforcement mechanism: the Controller of Budget (COB) will strictly reject any exchequer requests for salaries that are not submitted through the new integrated module.
An indepth look shows that this means that counties failing to migrate to the digital platform will face immediate funding blockages.
The steps taken serve as a final warning to county leadership teams, including Finance CECMs and County Assembly Clerks, to align their operations with national standards.
Centralizing of the approval process through the COB, the government ensures that only verified, legitimate payroll requests reach the taxpayer-funded exchequer, preventing further wastage and ensuring that the 35% wage bill ceiling is respected across the country.
Integrating these systems marks a turning point in Kenya’s devolved governance, moving toward a cleaner, more transparent public service payroll for all citizens.
