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Nakuru, Wajir, Nairobi, Siaya and Mandera recorded the largest shares of manual payroll payments among the counties flagged in the report. Meru, Elgeyo Marakwet, Kitui, Busia and Lamu were also among the counties that continued to process substantial payments outside the Human Resources Information System (HRIS).
The long-running debts have left suppliers, contractors and county workers waiting for payment, with Nairobi carrying the biggest share of the historical obligations at Sh49 billion.
The county had an approved supplementary budget of Sh25.65 billion, including Sh8.83 billion for development and Sh16.81 billion for recurrent programmes.
The committee, chaired by Luanda MP Dick Maungu, is examining Auditor-General Nancy Gathungu’s reports for the financial years under review, with the school accounting officers expected to respond to various queries.
According to the reports cited by The Standard, audits tabled before the National Assembly in August found cases involving unauthorised levies, spending without proper supporting documents, failure to collect outstanding fees, unexplained cash withdrawals, unapproved bank loans, weaknesses in procurement systems and questionable investments by some schools.
The National Assembly Committee on Constitutional Implementation Oversight says the current legal framework has left a large amount of public money outside the direct reach of the Controller of Budget, with 75 funds and levies at the national level and several others at the county level operating as potential blind spots.
Speaking to business executives at Silo Modern Farmhouse in Kansas City, Missouri, USA, on Friday, September 18, 2026, the Democracy for the Citizens Party (DCP) leader said delayed government payments were hurting Kenyans whose livelihoods depended on contracts with public institutions.
In the audit of the county executive for the year ended June 2024, the Auditor-General questioned the independence and effectiveness of the internal audit function. The audit noted that the internal audit unit was placed under the finance department and that its approved work plan had not been fully implemented.
Margaret Nyakang’o said agencies do not automatically qualify for funding simply because they claim they need money outside their approved allocations.
State House had the largest share of rejected requests among the institutions under the Presidency, with Sh7.3 billion denied from applications that had received Treasury approval.
The President also signed the Public Finance Management (Amendment) Bill 2025, bringing new provisions into the system used to manage public resources at both national and county levels.
The Auditor-General questioned the payment, saying KESSHA is a welfare organisation for school principals and is not recognised within the Government funding system.