Kenya risks vaccine shortages as Gavi funding phases out

Kenya’s progress in preventing childhood diseases like measles and rotavirus is at risk as donor support for vaccines phases out.

As donor support dwindles ahead of 2029, Gavi, the Vaccine Alliance has formally reminded the government to fulfill its co-financing obligation, demanding payment of Sh1.6 billion ($12.49 million) for the 2024/25 fiscal year, and due in full by June 2025.

The organisation warned that failure to meet this obligation could have serious consequences, including a disruption in vaccine supply, as there is a three-month lead time between payment and delivery.

Beyond stock shortages, Kenya risks being placed in default, which could block approval for new vaccine support and suspend disbursements to the Health System and Immunisation Strengthening (HSIS) programme.

If the arrears remain unresolved for more than a year, the country could further face suspension of already approved vaccine support.

“Gavi is sending this co-financing reminder letter as the Kenya co-financing obligation for 2024-2025 fiscal year totaling USD$ 12, 485, 880, remains fully outstanding. The 2024-25 co-financing obligation is due, in full by June 2025,” reads a section of the reminder privy to The Standard.

While Kenya would still be eligible for emergency support in case of an outbreak, exiting Gavi’s support would require a structured repayment plan, including settling current co-financing obligations and making an initial payment toward outstanding arrears.

Among childhood vaccines which can be affected include Human papillomavirus (HPV), Measles Rubella (MR), Malaria, pneumococcal conjugate vaccines (PCV), Pentavalent, Rota virus vaccine that prevents diarrhoea that causes neonatal deaths, Typhoid Vaccine (TCV) and Yellow Fever (YF).

Donor financing towards health has been dwindling and the resent US Stop work order and termination of contracts creating a funding gap and affecting service provision in HIV, TB, Malaria and Immunisation programmes as was earlier communicated by Health Cabinet Secretary Deborah Barasa.

Health advocates through Civil Society Organisations (CSOs) have pleaded with the government to expedite the payment of the obligations to avoid disrupting the country’s immunisation programme.

In an interview with The Standard, Dr Margaret Lubale, Health NGO’s Network (HENNET) executive director said there is need for the government to fast-track the process, warning that any financial gaps could lead to vaccine shortages, undermining years of progress in vaccination efforts.

“When a donor has had to remind us, about our promise. I think this does not speak well of us, as a country. We need to safeguard our children by ensuring the full financing of the immunization programme,” she said.

According to Lubale, the Kenya vaccine programme has been performing well due to the funding by both the government and donors.

“Financial gaps could lead to delays in procurement, distribution, it can be a catastrophe, we shall lose the gains we have made in this country,” said the health expert.

Lubale warned that if the immunisation is not fully financed, then lives of children are at risk. 

“Children are the future nation. It is very worrying to understand that there are pending Co-financing obligations, and this is why we are urging ministries of Health and Treasury to make good use of the promise. We need political will, we believe that Kenya is able to pay,” he stated.

Immunisation is among the programmes which rely heavily on donor funding, but with Kenya being a middle income country, the support is coming to an end by 2029, a move that require increased domestic financing for Kenya to be fully prepared for the transition from donor to self-sufficient.

Tharaka Nithi Governor Muthomi Njuki acknowledged the outstanding debt owed to Gavi and urged the National Treasury to allocate funds for Kenya’s vaccination programme to prevent a potential health crisis.

Speaking on March 12, 2025 during a high-level engagement attended by governors, the Ministry of Health, the National Assembly Departmental Committee on Health, and other stakeholders, Njuki who also chairs the Council of Governors’ Health Committee stressed the urgency of securing domestic financing following the freeze on donor aid.

The governor warned that failure to meet Kenya’s co-financing obligations could lead to a surge in paediatric deaths due to vaccine shortages.

“This issue affects every newborn in Kenya. Currently, Gavi is owed Sh1.4 billion, with payment due by June 30, 2025. If this amount is not included in the Budget Policy Statement submitted by the Ministry, there will be no vaccines for newborns by June this year,” Njuki cautioned.

He also noted that Gavi had planned to support Kenya’s vaccination programme until the 2029/30 fiscal year, and the government should have been prepared for the eventual phase-out.

“We cannot ignore this crisis as we transition from donor-funded programs. We must act now to ensure continued immunization for our children,” he added.

But even with donor support coming to an end, the need for government to adhere to the agreement with GAVI as well as ensure that we do not get vaccine stock outs, previous health sector (MTEF- Medium Term Plan), the government acknowledged that the vaccine program had previously experienced vaccine stock outs.

Kenya has been reporting vaccine stock-outs, namely measles vaccine, BCG, polio, rotavirus and tetanus vaccines, administered through KEPI.

The stock out was attributed to delayed disbursement of Sh1.2 billion co-financing funds by The National Treasury last year.

Shortage of the vaccines caused uproar among CSOs and media, which forced then Health CS Susan Nakhumicha to reach out to National Treasury leading to release of Sh1.5 billion for the commodities.

The ministry conducted mass polio vaccination and reached to 3.4 million newborns who were at risk of contracting polio in 2024.

Despite the ongoing challenges, Kenya’s expenditure on vaccines remains low, accounting for just 0.5 to 1 per cent of total health expenditures and 1 to 2 per cent of domestic government health spending.

Budget allocations for vaccination have also declined over the years for example in 2019/20, SH3.3 billion was allocated for vaccination, an amount that dropped to Sh1.4 billion in 2020/21.

In 2021/22, Sh14.3 billion was allocated, an amount that significantly reduced to Sh5.2 billion, with some Sh4.6 billion being allocated in 2023/24 and 2024/25.

With Gavi’s planned exit, Kenya will be required to fully finance its vaccination program using domestic resources, a transition that has raised concerns among stakeholders.

According to health financing expert Lubale, the co-financing policy was introduced to help Kenya transition smoothly from donor dependency over an eight-year period.

Initially, Gavi had planned to withdraw support by 2027, but this was extended to 2029.

“The more government gives, the less Gavi gives. Ideally, if Gavi was giving 100 per cent, with co-financing, the expectation is they would begin at 80 per cent, we give 20, they go 70, we give 30 they go down to a point they give zero, and we put 100 per cent as the county so that we cannot be able to say we are fully financing the immunisation program of this country out of domestic resource, and not relying on donors,” explained Lubale.

With donor support dwindling, experts warn that Kenya must urgently increase its domestic funding for vaccines to avoid potential immunisation crises in the coming years.