The Social Health Authority (SHA) owes Mombasa County Government about Sh1.2 billion, the devolved administration has revealed, sparking concern among stakeholders as the nationwide health financing system grapples with operational and payment challenges.
The disclosure was made at the Mombasa County Assembly, whose Health Committee is investigating challenges facing Coast General Teaching and Referral Hospital (CGTRH), the largest health facility in the Coast region serving six counties.
The funds are reportedly still held up at the national government level, leaving Mombasa’s public hospitals grappling with drug shortages, inadequate equipment and medics struggling to treat patients.
This is despite the county being lauded by William Ruto and Health Cabinet Secretary Aden Duale as the leading county in SHA registration, with more than 600,000 residents enrolled so far.
Recently, Mr Duale said Mombasa continues to lead nationally in SHA registration, demonstrating effective county leadership and strong collaboration with the National Government in advancing Universal Health Coverage (UHC).
The Sh1.2 billion arrears are said to cover payments owed to county-run facilities as well as support funds meant to bolster service delivery across Mombasa’s public health institutions.
Mombasa County Health Executive Dr Swabah Ahmed said CGTRH faces significant challenges because it has a high number of rejected claims.
Patients at the Coast General Teaching and Referral Hospital in Mombasa on February 25, 2026.
Photo credit: Kevin Odit | Nation Media Group
“This is because the diagnosis done by doctors does not match what is in the SHA system, or clerks are unable to interpret what the doctors have entered. This is largely what we are trying to resolve and correct at the hospital. We are training 20 medical officers and clinical officers in Nairobi to review these claims. They are processing about 300 claims per day,” said Dr Ahmed.
Dr Ahmed added that SHA owes CGTRH alone Sh700 million. She explained that once a claim is made, it is first processed through a digital system before being subjected to manual review for further verification.
Members of the Mombasa County Assembly have expressed frustration over the unpaid funds, warning that prolonged delays could negatively affect service delivery, staffing and the county’s ability to sustain essential health programmes.
Mombasa County Assembly Speaker Aharub Khatri questioned how the county could top SHA registration nationally while grappling with huge pending claims leaving patients in agony.
Meanwhile, doctors in Mombasa have called off their strike after reaching an agreement with the Mombasa County Government over key grievances.
The medics, under the Kenya Medical Practitioners, Pharmacists and Dentists Union (KMPDU), issued the strike notice a week ago following the suspension of Coast General Teaching and Referral Hospital Chief Executive Officer Dr Iqbal Khandwalla over alleged medical negligence.
They complained of stalled promotions, delayed confirmations, and what they termed as undue interference by local politicians in the management of health facilities.
Following a consultative meeting with Governor Nassir and county health officials, the parties agreed on a framework to address the concerns.
Union officials said the county government committed to fast-tracking long-overdue promotions and streamlining human resource processes to ensure fairness and transparency. They also welcomed assurances from the governor that there would be no political interference in hospital operations, emphasising that health institutions must remain professional and independent.
“The County has committed to the promotion of all eligible doctors across the following job groups: M to N, where 15 doctors will collect their letters immediately; N to P, where 33 doctors will collect letters on April 1, 2026,” said KMPDU Secretary General Dr Davji Atellah.
Dr Davji Bhimji Atellah, the secretary-general of the Kenya Medical Practitioners, Pharmacists and Dentists Union speaks to the media in Mombasa on March 3, 2026.
Photo credit: Kevin Odit | Nation Media Group
Others include Job Group P to Q, where 39 doctors are set to collect their letters on April 1, 2026, and another 39 on July 1, 2026. In Job Group Q to R, 17 doctors will collect letters starting April 1, 2026, while in Group R to S, four doctors will receive their letters by July 1, 2026.
On conversion to Permanent and Pensionable (P&P) terms, Dr Atellah said 64 doctors currently serving on contract will be transitioned effective June 1, 2026. He added that the County Government has committed to clearing all pending statutory deductions in full by September 1, 2026.
He noted that the union will remain vigilant to ensure the County Government adheres strictly to the agreed timelines.
Mr Nassir said the consensus was reached through dialogue and mutual respect, leading to the calling off of the strike. He added that his administration is committed to sustained engagement with doctors and all healthcare professionals to ensure that public hospitals reflect professionalism, stability and excellence in service delivery.
“To the residents of Mombasa, be assured that services across our health facilities will continue uninterrupted. Dialogue works and in Mombasa, we choose solutions over standoffs,” he said.
