Counties feel the strain as SHA arrears climb past Sh26 billion

County hospitals are facing a growing funding squeeze after unpaid claims under the Social Health Authority (SHA) rose to nearly Sh27 billion, leaving health facilities across the country waiting for reimbursements and raising concerns about the continuity of services.

New figures from the Controller of Budget show that county health facilities were owed Sh26.87 billion as of March 31, a sharp jump from Sh8.29 billion recorded at the end of December 2025.

The increase comes at a time when the government has consistently defended SHA, insisting that the health financing system is operating as planned and that hospitals are receiving payments.

The authority was rolled out in October 2024 as part of a major healthcare overhaul that replaced the National Health Insurance Fund (NHIF) with the Social Health Insurance Fund (SHIF).

At the time, the new model was presented as a solution that would improve access to medical care and ease the financial burden on Kenyans seeking treatment.

However, the latest report points to mounting payment delays that have left county facilities carrying billions of shillings in pending claims.

Nakuru County has recorded the highest amount owed. According to the report, the county is yet to receive Sh2.81 billion through the Facility Improvement Fund. Of this amount, Sh2.4 billion is owed by SHIF while Sh432.9 million relates to claims from the former NHIF.

Kakamega follows with Sh1.3 billion in outstanding claims, including Sh241.4 million owed by the defunct NHIF. Nyeri is owed Sh632 million by SHIF, while Mombasa is awaiting Sh596.7 million, comprising Sh357.1 million from SHIF and Sh239.6 million from NHIF.

Kiambu is owed Sh474.8 million, Garissa Sh429.48 million, Bomet Sh421.69 million, Homa Bay Sh390.3 million and Bungoma Sh358.5 million.

Other counties listed in the report include Kajiado with Sh343.8 million, Kitui with Sh333 million, Siaya with Sh287.47 million, Kisumu with Sh282.39 million and Elgeyo-Marakwet with Sh197.86 million.

Migori is owed Sh185.4 million, Nyandarua Sh183 million, Tharaka-Nithi Sh173.1 million, Kericho Sh165.7 million, Embu Sh163.74 million, Busia Sh134.8 million and Kwale Sh127.3 million.

The report further shows Baringo is owed Sh98.3 million, Marsabit Sh85 million, Machakos Sh68.25 million, Narok Sh67.4 million and Samburu Sh4 million.

Nineteen counties did not provide data to the Controller of Budget. These are Nairobi, Taita-Taveta, Nyamira, Nandi, Murang’a, Meru, Mandera, Makueni, Isiolo, Kilifi, Kirinyaga, Laikipia, Lamu, Tana River, Trans Nzoia, Uasin Gishu, Vihiga, Wajir and West Pokot.

Even as the debt continues to rise, government officials maintain that the scheme has made considerable progress since its launch.

Speaking on June 13, Interior Principal Secretary Raymond Omollo said SHA had registered more than 31 million Kenyans and contracted 11,034 health facilities across the country.

He added that the authority had settled over Sh147 billion in claims since October 2024, helping millions of Kenyans access healthcare services.

Despite those payments, contribution levels remain relatively low. Data presented by the government shows that about 4.8 million people are actively contributing to SHA. Of these, four million are salaried workers while 890,000 are from the informal sector. The contributions have generated a total of Sh70 billion.

The Kenya Medical Practitioners and Dentists Union and the Rural Private Health Association have previously faulted SHA over delayed payments and governance concerns. By August 2025, the organisations said the authority had paid approximately Sh53 billion against claims worth Sh96.2 billion.

The issue also featured before the Senate County Public Accounts Committee on June 16 when Homa Bay Governor Gladys Wanga disclosed that health facilities in her county were waiting for about Sh350 million from SHA.

While acknowledging that reimbursements had improved compared to the NHIF era, Wanga said delayed payments remained a major challenge for county hospitals.

“Every treatment you make; you file the claim but the money doesn’t necessarily come back to you on time. SHA owes us approximately Sh350 million for the health facilities in Homa Bay,” said Ms Wanga.

Nairobi Senator Edwin Sifuna told the committee that the growing backlog of claims was evidence that challenges remained within the system despite the billions of shillings invested to support SHA operations.