In a statement, the United Nations agency said that torrential downpours and flooding had destroyed over 300 health facilities in Madagascar, Malawi and Mozambique.
Cyclone Freddy dissipated last week after leaving a trail of destruction across southern Africa and causing hundreds of deaths.
Infrastructure damage has increased the risk of the spread of diseases such as cholera, malaria and COVID-19, the WHO said.
Cholera cases have doubled in Mozambique over the past week, according to the WHO, reaching 2,374 as of March 20 compared to 1,023 recorded the week prior.
Neighbouring Malawi, which is battling its worst-ever cholera outbreak, continues to see a drop in cases, the WHO said.
But storm damage risks slowing progress in the fight against the disease, the UN agency added.
"The impact of Cyclone Freddy is immense and deepfelt," WHO's Africa director Matshidiso Moeti was quoted in a statement as saying.
"Our priority is to ensure that affected communities and families receive health assistance for immediate needs as well as to limit the risks of water-borne diseases and other infections spreading," she added.
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