Cabinet Orders Mandatory Migration to New Payroll System.
Written by Boaz Nyabuto on July 1, 2026
The Cabinet has directed all Ministries, Departments, Agencies, and State Corporations to immediately migrate to a newly revamped Integrated Human Resource and Payroll System as part of sweeping reforms aimed at cleaning up government wage management.
The directive came on Tuesday, June 30, after a cabinet meeting chaired by President William Ruto at State House, Nairobi.
According to the cabinet, the migration is intended to centralise payroll processing across the public service, improve efficiency, and eliminate irregularities that have previously been flagged in government wage systems.
“The meeting also ordered the immediate implementation of a comprehensive payroll reform programme, including a Government wide audit of all remaining State Departments and public institutions, mandatory migration of all Ministries, Departments, Agencies and State Corporations onto the newly revamped Integrated Human Resource and Payroll System, enhanced cybersecurity, payroll data cleansing and validation, establishment of a disaster recovery site, and integration of payroll with other public financial management systems,” read a notice from a cabinet dispatch shared after the meeting.
The new system will enhance transparency in salary administration, strengthen oversight of public funds, and reduce vulnerabilities that have contributed to payroll fraud and unauthorised payments.
The meeting also ordered the immediate implementation of payroll reform programmes across the ministries amid concerns over weaknesses in payroll management systems.
The reforms, the cabinet said, will include a government-wide audit of all remaining State Departments and public institutions as part of efforts to eliminate payroll irregularities and strengthen accountability in public wage expenditure.
Other reforms include enhanced cybersecurity measures, payroll data cleansing and validation, and the establishment of a disaster recovery site to safeguard payroll information and ensure continuity of operations.
In addition, the government plans to integrate the payroll system with other public financial management platforms to improve coordination and accountability in public expenditure.
The move follows findings from a recent payroll audit that identified weaknesses in payroll governance across several State Departments, including irregular record alterations and gaps in internal controls.
It is worth noting that some agencies and county governments are already using the new system following earlier orders from the Public Service Cabinet Secretary, Geoffrey Ruku.
Ruku had earlier threatened to freeze salary payments to the state agencies that had not yet migrated to the system, noting that only a fraction of government agencies had been onboarded onto the HRIS platform, a figure he described as deeply troubling and unacceptable.
The CS in May 2026 gave human resource managers a two-month deadline to ensure their institutions complete the onboarding process, warning that failure to comply would have direct financial consequences for workers in those agencies.
The new directive from the cabinet will now strengthen this requirement and will see the government transitioning to the new payroll system, and therefore eliminating delays, fraud and system hitches traditionally flagged in the wage management system.
