The Controller of Budget also flagged inadequate funding for medical supplies. Some counties, including Kisumu, Vihiga, Nandi, Baringo, and Kitui, were found to have redirected funds away from medical commodities, leading to frequent stockouts, delayed services, and higher out-of-pocket costs for patients
By The Weekly Vision Team
Kenya’s counties are grappling with a KSh12.48 billion shortfall in health financing, owed to them by the Social Health Insurance Fund (SHIF) and the defunct National Health Insurance Fund (NHIF), according to a new report from the Controller of Budget, Margaret Nyakang’o.
The arrears consist of KSh7.46 billion from SHIF and KSh5.02 billion from NHIF, funds that county health facilities say are critical for sustaining service delivery. The report reveals that SHIF had approved claims worth KSh19.95 billion, but only KSh12.54 billion was settled, leaving a multi-billion-shilling gap.
Several counties have borne the brunt of the unpaid arrears. Nairobi is owed the most, with KSh301 million from SHIF and KSh937.39 million from NHIF. Other counties heavily affected include:
- Mombasa: KSh763.93 million (SHIF), KSh562.41 million (NHIF)
- Homa Bay: KSh455.21 million (SHIF), KSh267.04 million (NHIF)
- Kisumu: KSh334.16 million (SHIF), KSh336.24 million (NHIF)
- Bungoma: KSh236.43 million (SHIF), KSh840,000 (NHIF)
- Meru: KSh212.64 million (SHIF), KSh101.33 million (NHIF)
- Nakuru: KSh88.95 million (SHIF), KSh412.86 million (NHIF)
Nyakang’o has urged county leaders to work closely with the Social Health Authority (SHA) to recover the arrears and free up resources for service delivery.
The report also shows that as of June 2025, counties spent KSh141.78 billion on health, about 30 per cent of their total expenditure of KSh470.74 billion. Out of this, KSh97.45 billion went to health sector salaries, accounting for 44 per cent of total county wage bills.
Counties with the heaviest health wage burdens include:
- Baringo (67 per cent
- Nyeri (56 per cent)
- Trans Nzoia (55 per cent)
- Taita Taveta (54 per cent)
While the high allocation to staff pay underscores the importance of health workers, Nyakang’o warned that it limits resources for other essential needs such as drugs and equipment.
The Controller of Budget also flagged inadequate funding for medical supplies. Some counties, including Kisumu, Vihiga, Nandi, Baringo, and Kitui, were found to have redirected funds away from medical commodities, leading to frequent stockouts, delayed services, and higher out-of-pocket costs for patients.
Equally alarming is the KSh2.99 billion in pending bills owed to the Kenya Medical Supplies Authority (KEMSA) by counties. The biggest defaulters include Kilifi (KSh330.03 million), Nairobi (KSh225.16 million), and Tharaka Nithi (KSh146.9 million).
“The prolonged delays in settling these obligations have strained working relationships with KEMSA and other suppliers, eroded supplier confidence, and resulted in non-responsive bids during open tendering processes,” the report warns.
The financial strain threatens the stability of health service delivery across Kenya. If counties continue to struggle with unpaid claims, ballooning wage bills, and supplier mistrust, the risk of service disruption, drug shortages, and declining public confidence in county health systems will deepen.
The findings come at a critical time as the government pushes for the implementation of SHIF as the backbone of Kenya’s universal health coverage.
