NAIROBI, Kenya — Sixteen county governments have been flagged by the Controller of Budget (CoB) for failing to pay staff salaries in May and June, despite having received their full annual disbursements from the National Treasury.
In her latest report, Controller of Budget Margaret Nyakang’o revealed that counties including Nairobi, Mombasa, Nyandarua, Turkana, Narok, and Bungoma did not submit salary withdrawal requests to the Central Bank of Kenya.
Records show that Turkana, Narok and Bungoma last processed salaries in April, while Bomet, Kilifi, Kisumu, Machakos, Makueni, Mandera, Marsabit, Meru, Murang’a, Nyandarua, Tharaka Nithi and Mombasa stopped payments in May.
“Notably, out of the 47 county governments, 16 did not request their June 2025 salaries,” Dr Nyakang’o said, warning that the affected counties must make adequate provisions for employee compensation in the new fiscal year to cover arrears and avoid a repeat of the crisis.
The revelations come despite counties having received a combined Sh533.1 billion in 2024/25, comprising Sh387.43 billion in equitable share, Sh30.83 billion in arrears from the previous year, Sh24.86 billion in additional funding, Sh22.69 billion in carried-forward balances, and Sh67.3 billion from own-source revenue.
Wage Bill Pressure
The report underscores the persistent strain posed by salaries on devolved units. Counties spent Sh220.6 billion on compensation in 2024/25, up from Sh209.8 billion the previous year.
This accounted for 41.4 per cent of their revenues, breaching the 35 per cent legal ceiling.
Only seven counties managed to keep wage bills within the limit: Kilifi (24%), Siaya (26%), Tana River (27%), Nakuru (30%), Kwale (31%), Nandi (33%) and Nyandarua (33%).
Nyakang’o also flagged weaknesses in payroll management, noting that Sh10.7 billion — 5 per cent of all salary spending — was paid outside the government’s payroll system.
While lower than the Sh15.9 billion recorded the previous year, she warned that manual processing exposes public funds to misuse.
Health Sector Burden
The health sector continues to consume the lion’s share of county wage bills. Of the Sh141.78 billion counties spent on health last year, Sh97.45 billion went to staff salaries.
Some counties reported especially heavy burdens: Baringo spent over two-thirds of its entire wage bill on health workers, Nyeri allocated 56 per cent, Trans Nzoia 55 per cent, and Taita Taveta 54 per cent.
While acknowledging that channeling more resources to health improves service delivery, Nyakang’o cautioned that it limits investment in other critical areas.
She urged counties to collaborate with development partners to mobilise additional health funding and ease the fiscal squeeze.
