County health facilities are facing mounting pressure as delayed reimbursements from the Social Health Authority continue to pile up, leaving hospitals struggling to sustain day-to-day services and raising fresh concerns over the rollout of universal health coverage across the country.
A report covering budget implementation for the first half of the 2025/26 financial year by Controller of Budget Margaret Nyakang’o shows that public hospitals are still waiting for more than Sh8 billion in pending claims, a situation that is stretching already limited resources in devolved health systems.
“The mounting debt threatens the credibility of UHC. The delayed disbursements risk crippling services at the hospitals,” Nyakang’o’s says in her report.
Kisumu County carries the heaviest burden, with Sh1.87 billion still unpaid by the Social Health Authority. Nyeri follows at Sh633.6 million, Nakuru at Sh609.2 million, while Kiambu is owed Sh474.85 million.
Other counties with high outstanding amounts include Bungoma (Sh387.2 million), Mombasa (Sh334.3 million), Kakamega (Sh311.2 million), Siaya (Sh287.5 million), Kitui (Sh243.85 million), Kajiado (Sh232.33 million) and Garissa (Sh222.3 million).
Nyandarua is owed Sh219.7 million, Busia Sh204.87 million, Kwale Sh201 million, Embu Sh163.7 million and Kisii Sh111.9 million. On the lower end, Bomet is owed Sh54.2 million, Baringo Sh42.4 million, Narok Sh34.9 million and Migori Sh10.1 million.
Beyond Social Health Authority arrears, the report also highlights unpaid bills from the defunct National Health Insurance Fund, adding another layer of financial strain on county hospitals. Nakuru is owed Sh482.6 million, Mombasa Sh322 million, Kakamega Sh241.4 million, Migori Sh175.29 million, Kitui Sh89.1 million, Machakos Sh68.2 million, Baringo Sh67.3 million, Tharaka Nithi Sh22 million, Busia Sh20.5 million, Narok Sh18.9 million and Samburu Sh4 million.
The Controller of Budget notes that the accumulation of unpaid claims has slowed essential operations in hospitals, including procurement of drugs and medical supplies, affecting service delivery at the county level.
On April 22, Health Cabinet Secretary Aden Duale told senators that the government would begin clearing part of the outstanding obligations tied to the defunct Edu Afya programme under NHIF.
“The pending claims for Edu Afya schemes amount to Sh735 million,but the Sh116 million will be settled in two weeks,” the minister said. “The Sh619 million balance will be settled on availability of funds.”
He also said the National Treasury has set aside an additional Sh4 billion through a supplementary budget to help clear part of the outstanding NHIF liabilities, with the remaining balances expected to be settled in the 2026/27 financial year.
The Social Health Insurance Fund under the Social Health Authority was rolled out on October 1, 2024, with promises of faster reimbursements and improved transparency. However, hospitals continue to report delays in payments more than a year later.
Private and faith-based facilities have also raised concern over delayed settlements. The Kenya Conference of Catholic Bishops recently said SHA owes faith-based hospitals Sh5.7 billion, including rejected claims, while NHIF still owes Sh3.3 billion.
The transition from NHIF to the current system has faced criticism over system failures, slow claims processing, and limited coverage, forcing many patients to pay out of pocket.
Despite the challenges, the government says registration has grown, with 30.5 million Kenyans enrolled under the Social Health Authority by April 2026, as reforms continue to be implemented to stabilise the system and improve service delivery