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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).
Nairobi county blamed the delays on inadequate funding, failure to settle certified works, contractors pulling out of sites, procurement challenges and other issues linked to contracts.
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.
County governments are required to maintain their main bank accounts at the Central Bank of Kenya (CBK). Commercial accounts are allowed for specific purposes, but the County Treasury must first issue written authorisation.
The County Governments Implementation Review Report for the 2025/26 financial year shows that Meru used 79.04 per cent of its development allocation, while Trans Nzoia and Kirinyaga recorded 73.94 per cent and 73.89 per cent respectively.
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 County collected Sh15.54 billion in own-source revenue during the year, a 14.9 per cent increase from the Sh13.53 billion collected in 2024/25.
According to the Budget Implementation Review Report for the financial year ended June 2026, Nairobi accounted for the largest share of county travel expenditure after using Sh850 million during the period under review.
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.
The Health CS referred to Article 228 of the Constitution and the Controller of Budget Act, 2016, saying they clearly define the responsibilities of the Controller of Budget.
Speaking during an interview on September 17, 2026, Controller of Budget Margaret Nyakang’o listed the Social Health Insurance Fund, National Infrastructure Fund, Primary Healthcare Fund and Sovereign Wealth Fund among the funds that fall outside the Consolidated Fund.
She says weaknesses in expenditure controls, revenue shortfalls and reallocations during the financial year are undermining efforts to keep government spending within approved limits