Shots on the line: Thousands of children at risk as vaccine funds dry up

Marianne Wanjiru’s 19-month-old child is due for a second dose of polio, along with vaccines for influenza and typhoid. But vaccine supplies remain unstable.

Fortunately, Wanjiru is among the few mothers who can access private care through insurance. Many others are not as lucky.

“I’m anxious because the vaccine supply is unreliable. I’m fortunate to access them when needed, but I pity mothers who depend solely on public health facilities,” says Wanjiru, a social worker serving Njiru, Kibera, and Embakasi.

She adds that Bacillus Calmette-Guérin (BCG) vaccines have been consistently unavailable in the communities she serves, leaving newborns vulnerable.

The vaccine is given immediately after birth to strengthen a baby’s immunity and protect against tuberculosis (TB). The ongoing shortage is linked to a funding crisis within country’s immunisation programme, raising growing concern among parents whose children remain unvaccinated.

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“I can afford vaccines because I am employed, but what about someone who can’t even afford food?” poses the mother.

Vaccine financing

Her concerns reflect those of thousands of mothers whose children risk missing critical vaccines due to delays in government funding for immunisation efforts.

As fears over vaccine supply instability grow, data from the Ministry of Health shows a troubling rise in childhood TB cases.

In 2023, at least 139,000 people developed tuberculosis in Kenya—17,000 of them were children. The country has also reported sporadic outbreaks of measles, further underscoring the urgency of consistent vaccine access.

Over the years, Kenya has heavily relied on donors for vaccination programme, but with its elevation to a middle income country by the World Bank, the country is expected to fully pick up the programme

Kenya’s vaccine financing has seen significant progress in recent years, with government funding covering between 21 per cent and 50 per cent of routine immunisation expenditures from 2017 to 2022.

According to the budget appropriation for the last financial years, the budget allocation to immunisation has gradually been reducing, leaving gaps in immunisation coverage. For example the National Treasury Mwananchi reports indicate a flat immunisation budget for three consecutive years at only Sh4.6 billion.

Health NGOs’ Network (HENNET) executive director Dr Margaret Lubaale says whereas a step towards achieving self-sufficiency has been made, the country still faces challenges in fully funding its immunisation programmes.

In an interview with the Standard on Sunday, the health advocate notes that government spending on vaccines accounts for just 0.5 per cent to 1 per cent of Kenya’s current health expenditures, and one per cent to two per cent of domestic general government health expenditures.

With the expectation that the country will transition from GAVI, the Vaccine Alliance support by 2029, she observes that the entire immunisation budget will soon need to be funded domestically.

Sadly, in a recent meeting held between Ministry of Health and senior GAVI officials on May 5, 2025, the government reported that they were negotiating for the transition period to be extended to 2035.

Lubaale says that while this allows the government room to plan better, it is also a sign of government’s poor planning with the current transition, which had been communicated years ago.

“Requesting for extension is an indication of the government placing the critical focus on child health to donors,” says Dr Lubaale.

The World Health Organization (WHO) estimates that immunization prevents 4.4 million deaths annually.Kenya has been an active participant in the GAVI initiative, which has greatly expanded access to vaccines and strengthened the country’s immunisation infrastructure.

The country’s vaccination programme is, however, at brink, risking gains made over the years if it default paying Sh1.6 billion obligations to Gavi, under 2024/25 financial year.

Delays in meeting co-financing obligations have stalled progress in vaccination programme, says Lubaale.Under its agreement with the government, Gavi co-finances the immunisation budget— the government covers a portion while Gavi funds the rest.

Co-financing, a formal commitment by Kenya to support vaccine procurement, is vital to sustaining the national immunisation programme.

For the 2024–2025 fiscal year, the required co-financing amount is USD $12.49 million, but no payments have been made to date.

The outstanding balance is due in full by June 30, 2025, and failure to meet this deadline could jeopardize the country’s vaccine supply, as outlined in the Kenya-Gavi co-financing agreement.

“A delay in payments can lead to vaccine stock-outs, given the three-month lead time between payment and delivery of doses,” warned Lubaale.

According to experts, delays in vaccine funding are not only lowering immunisation rates but also leaving children vulnerable to preventable diseases such as diarrhoea, polio, measles and pneumonia.

Kenya has faced persistent shortages of infant vaccines, which experts attribute to poor planning and the government’s failure to account for population growth.

Last year, the country experienced stock-outs of key vaccines, including BCG, measles, polio, rotavirus, and tetanus. The jabs are given to newborns to immunise them against six killer childhood diseases, namely TB, polio, diphtheria, whooping cough, tetanus and measles among others.

In 2022, some newborns died in the country following shortage of rotavirus that prevents diarrhoea cases.

To prevent deaths, WHO recommended having rotavirus vaccine included in every country’s national immunisation programme in 2009, and it would be considered in immunisation programme in 2014.

In 2018/19 data, at least six per per 1,000 live births, under-five deaths were due to pneumonia, accounting for 15 percent of child deaths in the country.

Health civil society groups are urging the National Treasury to expedite payment of Kenya’s vaccine co-financing obligations to avoid disrupting immunization efforts.

In a statement, they warned that delays could lead to vaccine shortages and reverse gains made in immunisation coverage. “We urge the government to honor its co-financing commitment to ensure smooth vaccine rollout, meet immunisation targets and maintain strong ties with key donors,” said Faith Ndung’u, HENNET Advocacy Manager.

Immunisation is one of the health programmes that heavily rely on donor funding—a growing concern as Kenya’s classification as a lower-middle-income country requires it to gradually increase domestic financing to sustain progress.

The country’s routine childhood vaccinations are administered under the Kenya Expanded Programme on Immunization (KEPI).

UNICEF has been at the forefront of addressing zero-dose children—those who have never received a single vaccine and remain highly vulnerable.

“The government of Kenya with the support of GAVI, The Vaccine Alliance, worked on enhancing vaccine supply and logistics, enabling better coverage in undeserved areas,” says UNICEF Kenya’s Chief of Health, Luigi D’Aquino.

According to routine information systems, half of zero dose children are found in 14 counties which include Nairobi, Mombasa, Kakamega, Kisii, Trans Nzoia, Kericho, Bomet, Uasin Gishu, Bungoma, Homa Bay, Kilifi, Kitui, Nandi and Wajir.

Prof Ruth Nduati, a paediatric reaffirms that vaccines protect children from well known childhood illnesses that cause death in children.

“Polio causes disability,” says Nduati. “If we do not vaccinate our children, they will start getting sick,”

Amid anxiety crippling in supply of vaccines, the government remains reluctant to comment on the issue.

Director of Health Dr Patrick Amoth has maintained that the ministry is in discussion with the National Treasury to mobilise resources for payment.