The National Treasury has issued a new directive that will significantly impact how county government salaries for April 2026 are processed, in a move aimed at improving payroll management across state institutions.
In a circular dated April 8, 2026, Treasury Principal Secretary Chris Kiptoo directed all County Executive Committee Members for Finance and County Assembly Clerks to process April payroll exclusively through the integrated HRIS-Kenya Payroll System and IFMIS platform.
It is worth noting that the Integrated HRIS-Kenya Payroll System manages government employee records and salaries, while the Integrated Financial Management Information System (IFMIS) handles budgeting, procurement and tracking of public funds.
According to Kiptoo, the integration of the two systems is designed to streamline statutory deductions and enhance efficiency in public finance operations.
Kiptoo noted that the integration has already been piloted successfully across several national government state departments and some county assemblies, and as a result, all accounting officers have been urged to fully comply.
“Therefore, to support these constitutional entities in executing their mandatory duties, it is prudent for all accounting officers to comply by utilising the Integration Module,” Kiptoo directed.
The PS made it clear that the Office of the Controller of Budget will only approve exchequer requests for salaries submitted through the integrated module.
This therefore means that any county officers’ salaries not processed through the new integrated system risk delays or rejection in the April 2026 payroll.
“The purpose of this letter, therefore, is to bring this matter to your attention and request you to process your April 2026 payroll through this Integration Module,” the PS added.
While making the announcement, Kiptoo emphasised the need for compliance to ensure smooth salary processing and adherence to public finance regulations.
The move is part of the Public Finance Management Act, 2012, aimed at improving accountability and efficiency in the management of public funds across both national and county governments.
County officials are now expected to align with the new system immediately to avoid disruptions in salary disbursement for April this year.
Audit Reveals How Counties Spend Billions Outside Approved Payroll System
The latest announcement follows reports by the Auditor-General, Nancy Gathungu, who revealed that over Ksh33 billion in the 2024/25 financial year alone may have been lost to ghost workers in counties, raising fears of widespread payroll fraud.
The Audit flagged Ksh978 million paid to suspected ghost workers after nearly 600 county employees failed physical verification across 26 counties.
The counties of Machakos, Mandera and Kajiado topped the list as payroll integrity concerns deepen.
According to the Auditor-General’s findings, several counties made payments to staff who were not captured in the official payroll system, contrary to public finance regulations.
In some cases, counties paid casual workers, contract staff and alleged ‘special duty’ officers through vouchers and bank transfers without proper documentation or approval from the County Public Service Boards.
The auditor noted that the names of some beneficiaries did not appear in any official employment records, making it impossible to establish whether the recipients were genuine employees-Kenyans.co.ke.