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Saturday, September 19, 2026

El Niño: Health ministry maps high-risk counties in Sh2.9bn plan

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A flood-control channel in Simbi Kogembo, Rachuonyo North, on September 12, 2026. 

Photo credit: George Odiwuor I Nation Media Group

By  Hellen Shikanda

Health and Science Reporter

Nation Media Group

The Health ministry has proposed a budget of Sh2.9 billion to cater for the preparedness and response to El Niño for the period between October and December this year.

In a draft Health Sector El Niño Contingency Plan seen by Nation, the ministry has identified five key areas of intervention that will help ensure that the health sector works seamlessly despite the anticipated challenges.

Some of these interventions include supporting a joint health sector vulnerability and risk assessment, mapping anticipated flood high-risk counties, prepositioning and distributing essential drugs, key medical commodities and supplies, buying commodities for water and sanitation, enhancing mechanisms to support cross-cutting flood response interventions, and facilitating flood and drought coordination, activities, structures and forums at all levels.

In its budget, pharmaceutical and non-pharmaceutical products received the largest allocation, followed by enhancing laboratory services and disease surveillance.

The ministry also plans to collaborate with other sectors and ministries such as water and sanitation, energy, livestock, education, telecommunications and ICT, transport, security and the Kenya Defence Forces.

“In anticipation of the impending El Niño rains, a comprehensive and proactive approach is essential to mitigate the potential public health emergency in Kenya. Timely interventions in weather monitoring, health infrastructure, community education, and emergency response coordination can significantly reduce the impact on the health and well-being of the population,” indicated the draft plan.

They also mapped out key impacts on human life that the El Niño rains may have.

These include trauma and drowning, different disease outbreaks and public health risks, mental health challenges, population displacement and an increased risk of aflatoxin poisoning.

They also anticipate a fractured health system, including constraints on routine referrals of medical emergencies, power disruptions, flooding of some facilities and supply chain disruptions that could lead to depletion of essential supplies.

Data from the National Disaster Operations Centre shows that during the 2023 El Niño, there were 175 deaths, 40 missing persons and 242 injuries recorded.

About 60,367 households were affected, resulting in the displacement of nearly 384,216 individuals into 170 internally displaced persons' camps. Their data also shows that about 5 per cent (64 out of 1,434) of health facilities across 11 counties became inaccessible.

During that period, climate-sensitive disease threats emerged, including cholera, with 409 cases and four deaths affecting five out of the 47 counties. Lamu recorded the highest number of cases, with 80 per cent, or 326 people, affected.

There were seven human Rift Valley fever cases reported in Marsabit, 71 per cent (five), and Wajir, 29 per cent (two), alongside livestock cases.

Malaria upsurges were documented in Wajir (373), Marsabit (975) and Kitui (535).

Social vulnerabilities also worsened, with 50 gender-based violence cases reported across nine out of the 47 counties.

Health Principal Secretary in charge of Public Health Mary Muthoni also advised that every county has to maintain basic preparedness, especially those facing a higher risk of flooding, landslides, disease outbreaks, injuries or malnutrition, which should strengthen their readiness without delay.

Public Health Principal Secretary Mary Muthoni. 

Photo credit: File | Nation Media Group

“We are acting early and together. We have learnt from previous El Niño emergencies, and our goal is to prevent avoidable deaths, disease outbreaks and disruption of health services,” she said.

Dr Daniel Lang’at, the National Head of the Division of Disease Surveillance and Response (DDSR) at the Health ministry, told Nation that their division has done what is expected based on the forecast they received from the Kenya Meteorological Department.

“Our disease surveillance team is on the lookout for water-borne diseases like cholera and typhoid, and vector-borne diseases like malaria, because they are likely to come with the floods,” he said.

“What we learnt from the previous El Niño seasons is that if we do things early enough, then it makes a lot of sense. We will continue doing what is expected of us, but we want to take this to the community level. That is why we are using community health promoters to give us the signals when things are not good,” he explained.

Onesmus Musau, Programme Lead for HIV Prevention, Testing, Adherence and Retention on Treatment at LVCT Health, told Nation that El Niño should also be looked at through a health security lens.

“We know when it rains, there are those disruptions that come in the health sector that affect service delivery. We have roads that are cut, and patients are not able to move from their houses to get to the health facilities,” he said.

At LVCT, they implement health security programmes, especially when they anticipate new health threats.

“We are looking at preparedness in categories including laboratory resilience, service delivery, risk communication, healthcare workforce and disease surveillance,” he explained.

Onesmus told Nation that for conditions like HIV, continuity of services must be ensured so that no client misses life-saving medication for their treatment.

“We expect that clients will visit health facilities and collect their drugs and also have tests to track treatment outcomes. We are recommending that facilities should manage client appointments so that we have more clients coming for their appointments before the rains,” he said.

“If you have an appointment, bring it a bit earlier, especially if you come from a flooding zone. When the rain comes and we have defaulters, we are using facilities to organise outreaches. We are urging counties to prepare community health promoters in case there are defaulters,” he added.

He also said that there are a lot of rumours and misinformation that come when there is flooding. Together with the ministry, they are setting up systems to track such things so as to dispel them in advance.

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