According to the Burundi's health minister, Dr Josiane Nijimbere, more than 3,700 people have died from the mosquito-borne disease since 2016.
"There is an increase of 13% of the cases related to malaria," she said adding that this "is why we have decided to declare the disease as an epidemic."
She singled out Kirundo, Muyinga and Kayanza in northern Burundi and Cankuzo in the east as the areas in which an increase in the number of people suffering from the disease have been reported.
The situation is further compounded by climate change and prolonged drought leading to people going without food, she said.
"The World Health Organisation (WHO) priority now is to work with the Burundi ministry of health to finalise the outbreak response plan, engage in resource mobilisation and provide technical support including deploying malaria specialists," Dr Walter Kazadi Mulombo, the WHO representative in the country told The EastAfrican.
About $3.1m is needed for the response plan, according to both government and WHO.
Burundi previously declared a malaria epidemic in 2002.
According to WHO, last year 212m malaria cases were reported globally with 429,000 deaths recorded.
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