By Lenah Bosibori
The Ministry of Health has activated its El Niño preparedness plan in 18 high-risk counties as Kenya braces for above-normal rainfall expected during the October–December 2026 rainy season.
The heavy rains could trigger flooding, contaminate water sources, and disrupt health facilities and supply routes, increasing the risk of cholera and other diseases, malaria, injuries, displacement, and malnutrition.
The ministry is now calling on counties and health partners to strengthen preparedness and ensure that essential services remain available during the rainy season.
Speaking in Nairobi on Wednesday during a stakeholders’ meeting co-convened by the Ministry of Health and the Health NGOs Network (HENNET), Public Health and Professional Standards Principal Secretary Mary Muthoni said the country must urgently move from planning to action.
“Our focus must now shift from planning to operational readiness,” Muthoni said.
She said the ministry has developed a Health Sector El Niño Contingency Plan, strengthened disease surveillance and outbreak response, and established an Incident Management Team and Steering Committee to coordinate preparedness efforts.
Muthoni said high-risk counties should ensure essential medicines and health commodities are pre-positioned before the rains intensify.
She also called for rapid response teams to be prepared in advance, referral and emergency transport systems strengthened, and water, sanitation and hygiene systems protected.
“We need continued partnership in prevention, preparedness, surveillance, early detection and rapid response while ensuring continuity of essential health services during emergencies,” she said.
Flooding and disease risks
The anticipated rains could place additional pressure on health services, particularly in areas vulnerable to flooding.
Flooding can cut off communities from health facilities and disrupt the movement of medicines and other essential supplies. Contaminated water sources can increase the spread of waterborne diseases, while stagnant water can create favorable conditions for malaria transmission.
The World Health Organization has also warned that flooding can contaminate drinking water and sanitation systems, making it harder for people to reach health facilities and access medicines.
Muthoni said Kenya’s experience with Ebola, Mpox and other public health emergencies had demonstrated the need to prepare before a crisis occurs. “Preparedness cannot begin when an emergency occurs,” she said.
She called for continued investment in disease surveillance, laboratory systems, health workers, supply chains and emergency response systems.
The ministry also wants essential health services to continue during emergencies so that communities can access routine care even as authorities respond to disasters and disease outbreaks.
Muthoni urged development partners, civil society organisations, private-sector actors, professional bodies, academia and counties to work with the ministry to identify and close remaining preparedness gaps.
She said partner support should complement government preparedness structures and align with national and county priorities.
The meeting was co-convened by the State Department for Public Health and Professional Standards and the Health NGOs Network-Kenya (HENNET).
Muthoni said partnerships should move beyond meetings and result in clear commitments, defined responsibilities, realistic timelines and measurable outcomes. “Our health agenda is too important for commitments to remain on paper,” she said.
She also called for greater follow-up on commitments made during the Kenya Health Summit, saying the success of health sector reforms would ultimately be measured by implementation and results.
The ministry also urged stakeholders to participate in the Kenya Public Health Conference (KEPHIC) 2026, scheduled for October 26–30.
Muthoni said the conference would provide an opportunity for government, counties, health partners, civil society, academia and the private sector to share evidence and innovations and strengthen collaboration around Kenya’s public health priorities.
The anticipated El Niño comes after flooding affected 27 counties during Kenya’s March–May 2026 long rains, according to the WHO, highlighting the need for early preparedness ahead of the next rainy season.
As the October–December rains approach, the Ministry of Health is urging counties and partners to ensure that preparedness measures are translated into action before flooding and disease outbreaks occur.
Muthoni said the focus should be on moving from dialogue to action, from commitments to implementation, and from implementation to results.
Dr. Aaron Kimeu, Head of Health Emergencies and Disaster Risk Management at the Ministry of Health, said the ministry has established priority pillars to anchor its emergency response, focusing on disease surveillance, outbreak control, multi-agency coordination, water and sanitation (WASH), essential health supplies, and laboratory testing capacity.
“Our emergency response framework rests on six critical pillars: active surveillance and outbreak control, coordinated disaster response, water and sanitation safety, uninterrupted supplies of health commodities, and expanded laboratory testing capacity,” Dr. Kimeu said. “Strengthening these areas ensures that when emergencies strike, our health systems can detect threats early and respond rapidly without breaking down.”
