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By Victoria Musimbi
Nairobi, Kenya: Faith-based hospitals in Kenya are struggling to sustain their healthcare services amid more than KSh10 billion in unpaid claims, costly digital compliance requirements and proposed regulatory penalties.
The concerns were raised during a high-level Faith Community Leadership Dialogue organised by the Christian Health Association of Kenya (CHAK), bringing together representatives from the National Council of Churches of Kenya (NCCK), World Vision, St. John’s Community Centre, the PCEA Health Board and Mission for Essential Drugs and Supplies (MEDS), among other organisations.
Presenting their concerns during a press briefing NCCK Chairman Rev. Dr. Elias Otieno Agola called on the government to address the financial and regulatory challenges facing faith-based health facilities, warning that the reforms could undermine healthcare delivery, particularly in underserved communities.
Faith-based and mission hospitals said they account for approximately 40% of healthcare delivery in Kenya and are owed more than KSh10 billion in claims inherited from the defunct National Hospital Insurance Fund (NHIF) and delayed reimbursements under the Social Health Authority (SHA).
“Many of our facilities depend on public health insurance for up to 90% of their revenue. When payments are delayed, hospitals struggle to pay suppliers, purchase essential medicines and meet staff salaries,” said Dr. Agola.
The financial strain has forced some facilities to turn away patients or demand out-of-pocket payments, raising concerns about access to healthcare for vulnerable communities.
The challenges have also extended to the transition to certified Hospital Management Information Systems (HMIS) under the Digital Health Agency (DHA).
Only 190 of the 518 faith-based facilities, representing 37% had completed migration from the temporary SHA provider portal, compared with all public health facilities from Levels 2 to 4.
The transition costs between KSh600,000 and KSh1 million annually, adding to the financial burden on facilities.
“We support the move towards digital health systems, but the cost of migration and technical challenges are making it difficult for some facilities to comply within the set timelines,” Agola said.
The Ministry of Health extended the migration deadline to November 30, 2026, warning that the provider portal would be deactivated on that date and non-compliant facilities risk losing their SHA contracts.
The organisations also raised concerns over requirements under the 2026–2029 Hakika SHA provider contracting cycle. Facilities must submit KMPDC licences, KRA and NSSF compliance certificates, banking documents and registration with the Office of the Data Protection Commissioner, among other requirements. Levels 4 and 5 facilities must also provide audited financial statements.
Dr. Agola called for flexibility in implementing the requirements, warning that administrative and financial barriers could lock some faith-based facilities out of the contracting process.
“Facilities should not be excluded from providing healthcare because they are unable to meet costly or duplicative administrative requirements. There is a need for consultation and flexibility,” he said.
Another concern is the proposed Quality Healthcare and Patient Safety Bill, 2025, which introduces penalties of up to KSh50 million, imprisonment for up to 10 years, or both for administrators and institutions found guilty of substandard care or gross negligence.
While supporting efforts to strengthen patient safety and accountability, the leaders warned that the proposed penalties could disproportionately affect financially constrained facilities and risk forcing some to close.
Dr. Agola urged Parliament to engage healthcare providers before passing the legislation, saying patient safety measures should take into account the circumstances of different health facilities.
“We support accountability and better standards of care, but the law should also consider the realities facing facilities, particularly those struggling financially. Regulation should strengthen healthcare delivery, not undermine institutions that serve vulnerable communities,” he said.
The participating organisations called for sustained engagement between the government, regulators and healthcare providers to ensure that ongoing reforms strengthen the health system without compromising access to essential services. They emphasised that faith-based facilities must be recognised as important partners in achieving universal health coverage.
