Fresh data by the government has unmasked how forged academic certificates, off-payroll salary payments and delayed digital reforms continue to bleed state coffers.
The revelations come as detectives investigate a suspected Sh6.5 billion payroll fraud, highlighting long-standing weaknesses in personnel management that have persisted despite repeated government promises to clean up the public service.
An analysis of the latest Public Service Commission (PSC) evaluation paints the picture of a government payroll system riddled with loopholes, weak oversight and fragmented human resource management systems that continue to nurture fraud.
The findings also reignite the debate on Kenya's expanding public wage bill, which has remained one of the country's biggest fiscal challenges.
According to the latest Salaries and Remuneration Commission (SRC) data, compensation for public servants consumes 41.8 per cent of total government revenue, way above the internationally recommended threshold of 35 per cent.
Kenya remains among African countries with one of the highest public sector wage burdens.
The total public wage bill stands at roughly Sh1.24 trillion, supporting over one million public workers.
It has consistently exceeded Sh1 trillion annually across the national and county governments, placing enormous pressure on public finances.
The latest payroll anomalies come at a time when President William Ruto's administration has repeatedly pledged to eliminate ghost workers and digitise government human resource systems.
Ruto has on several occasions said every shilling lost through corruption and payroll fraud denies Kenyans essential public services, insisting that technology must become the government's strongest weapon against theft of public resources.
Public Service Cabinet Secretary Geoffrey Ruku has also maintained that payroll integrity remains central to ongoing reforms in government.
"We must ensure that every public officer is properly identified, verified and paid through transparent systems. Public funds must only pay genuine public servants," Ruku said while outlining reforms aimed at improving accountability.
Last week, the CS handed the report to investigative agencies to track, arrest and recover ghost workers looting public coffers.
His ministry has continued pushing state corporations and county governments to fully migrate to the Human Resource Information System-Kenya (HRIS-Ke), which is expected to eliminate duplicate records, ghost workers and unauthorised salary payments.
However, the PSC findings show the reforms remain far from complete.
The commission's review reveals glaring discrepancies between official personnel records and actual staffing levels across government institutions.
Official biodata records captured 244,208 employees, yet institutions submitted employment records covering 260,202 officers.
16,000 ghost workers
The unexplained difference of 15,994 officers, representing 6.1 per cent of the workforce, raises fresh questions over the existence of thousands of employees who cannot be reconciled within government records.
While the PSC stops short of declaring them ghost workers, experts say such variances create significant opportunities for fraudulent salary payments.
The inconsistencies are particularly pronounced in public universities, where staffing registers exceeded employees physically in post by 4,076 officers.
State corporations and Semi-Autonomous Government Agencies (SAGAs) recorded another unexplained variance of 3,586 employees.
Although ministries and state departments showed a surplus of 1,380 officers, the PSC attributed this partly to the exclusion of over 30,700 prison officers from the primary staff register.
Even more concerning, employment terms for 32,933 officers, representing 13.5 per cent of staff, were not indicated in institutional returns, making it impossible for the commission to verify whether they were legitimately employed or even eligible for pension benefits.
Public Service Principal Secretary Jane Imbunya said proper personnel records are fundamental to accountability, noting that digital human resource systems are critical in ensuring government only pays legitimate employees.
4,000 paid outside payroll
The PSC review also uncovered widespread disregard for government directives requiring all public officers to be paid through centralised payroll systems.
Instead, 72 public institutions admitted paying 3,868 officers through off-payroll arrangements.
The practice undermines the National Treasury's controls designed to prevent unauthorised payments and makes independent verification extremely difficult.
Kenyatta National Hospital (KNH) recorded the highest number of officers receiving salaries outside the official payroll, with 1,136 employees.
It was followed by Moi University with 695 officers, Kenya Forest Service with 385, and Kenya Wildlife Service with 310.
The duration of the irregular payments suggests systemic failures rather than temporary administrative delays.
At least 778 officers, representing 20.1 per cent, had remained on off-payroll salary arrangements for more than one year.
For another 2,157 officers, accounting for 55.8 per cent, institutions failed to disclose how long the payments had been made, creating what auditors describe as major gaps in expenditure records.
The continued use of parallel payroll systems comes despite repeated Treasury directives requiring all government salaries to pass through centralised systems.
Fake certificates
The PSC also uncovered extensive academic fraud within the public service.
Verification exercises identified 561 forged academic and professional certificates that had been used to secure employment or promotions.
The Kenya Certificate of Secondary Education (KCSE) accounted for almost half of the forged documents, with 267 fake certificates detected.
The Kenya Revenue Authority (KRA) recorded the highest number of forged credentials, reporting 141 fake certificates, followed by the Postal Corporation of Kenya with 71.
The commission says the findings expose serious weaknesses in recruitment, promotions and internal verification processes.
More worrying, nearly 28.3 per cent of institutions that discovered officers with fake certificates failed to take disciplinary action.
Among those cited were the Office of the Controller of Budget, the Kenya Bureau of Standards (KeBS), the Kenya Meat Commission, and the Social Health Authority (SHA).
The PSC warns that failure to dismiss such officers effectively allows continued payment of public money to employees who secured jobs fraudulently.
Digital reforms roadblock
Successive administrations have viewed digitisation as the ultimate solution to payroll fraud.
The Human Resource Information System-Kenya (HRIS-Ke) was designed to integrate personnel records, payroll management, promotions and employee verification under one platform.
Every public institution was required to migrate to the system by June 30, 2025.
Yet the latest evaluation shows 81.8 per cent of institutions had failed to comply with the deadline.
The failure leaves personnel records fragmented across multiple systems, making reconciliation of staffing records difficult and allowing irregular payroll practices to continue.
Ruku has repeatedly insisted that complete digitisation remains non-negotiable if government is to eliminate ghost workers and improve service delivery.
Wage bill under pressure
The payroll irregularities come as Kenya struggles to contain a rapidly expanding wage bill.
The Salaries and Remuneration Commission has repeatedly warned that compensation costs remain unsustainable and continue to crowd out funding for development projects.
It has consistently called for rationalisation of public institutions, better workforce planning and elimination of duplicate functions.
SRC commissioner Michael Kingi has argued that growth in public employment must be matched with productivity improvements to ensure taxpayers receive value for money.
Human Rights lobby groups say that unchecked growth in personnel expenditure leaves less money for infrastructure, healthcare, education and other essential public services.
Opposition leaders led by Wiper's Kalonzo Musyoka and Kiharu MP Ndindi Nyori have equally questioned the government's commitment to tackling payroll fraud.
They insist that eliminating ghost workers should precede any discussion on introducing new taxes or increasing borrowing.
Many lawmakers have maintained that cleaning up the payroll could save billions of shillings annually and reduce pressure on taxpayers.
Apart from a well orchestrated runaway payroll fraud that has seen children aged as low as seven years paid over years, personnel management is also proving costly in court.
The PSC review shows legal claims against public institutions rose sharply to Sh66.4 billion, up from Sh43.8 billion the previous year.
Labour and employment disputes accounted for 610 cases, representing 13.2 percent of all litigation involving government agencies.
At the same time, government is struggling to pay some genuine employees.
Outstanding salary arrears stood at Sh251.4 million by June 30, 2025.
KNH, ironically the institution with the highest number of off-payroll employees, also accounted for 72.5 per cent of officers whose salaries remained unpaid.
Even institutions mandated to enforce accountability have not escaped scrutiny.
Auditor-General Nancy Gathungu flagged unresolved issues within the Public Service Commission itself, including irregular recruitment, retention of staff beyond mandatory retirement age and engagement of retired officers as consultants.
Auditors also questioned whether taxpayers obtained value for money from the commission's Integrated Management Information System.
More than Sh67.8 million has been spent on the project since 2015, yet it had still not moved from testing to full implementation.
Gathungu says that weak internal controls, delayed implementation of audit recommendations and poor record management remain among the leading causes of financial losses across government.
The PSC has now issued strict timelines to restore integrity within public service management.
It had directed all state agencies to migrate fully to HRIS-Ke and process all salaries exclusively through the centralised payroll system by June 30, 2026.
There was no update yet on this directive by the time of going to press.
Institutions were also supposed to conclude disciplinary action against officers found using forged certificates and review staffing establishments to eliminate redundant positions and align workforce numbers with actual workloads.
The reforms are part of broader efforts by the government to improve efficiency and restore public confidence in the civil service.
Yet the scale of the challenge remains enormous.
Overall compliance with public service standards declined marginally from 43.8 per cent to 43.5 percent, indicating that reforms have largely stagnated.
Unless government succeeds in closing payroll loopholes, strengthening verification systems and fully digitising personnel records, HR specialists warn that Kenya's already strained public finances will continue financing workers who exist only on paper.
"Every ghost worker, forged certificate and unauthorised salary payment represents classrooms not built, medicines not purchased, roads left unfinished and essential services denied to millions of Kenyans," Kenya Human Rights Commission (KHRC) says in it's latest report.
