The disease has infected 1.8 million people in the East African nation so far this year, senior government officials say.
A malaria epidemic has broken out in Burundi, killing more than 700 people so far this year and leaving over a million infected.
From January 1 to March 10 this year, 1.8 million infections were registered in Burundi, according to the World Health Organization (WHO).
"Burundi faces a malaria epidemic," the health minister of the East African nation, Josiane Nijimbere, said while commenting on the WHO report.
"Some 700 deaths" have been registered since January, the minister added.
Nijimbere said that the latest figures on the people infected with the mosquito-borne disease constitute a 17 percent increase from the same period last year.
In 2016, an estimated 8.2 million people were infected and 3,000 people died in mountainous Burundi, which is home to around 11 million people.
Shortage of medicines
UN officials and medical sources said that Burundi's stock of anti-malaria medication is nearly empty.
Nijimbere put the cost of fighting malaria at $31 million while appealing for donations to help fight the disease.
She attributed the rise in infections to climate change, increased marshland for rice-growing and the population's misuse of mosquito nets.
Burundi has been in turmoil since President Pierre Nkurunziza in 2015 successfully pursued a third term that many called unconstitutional.
Hundreds have died and nearly 500,000 people have fled the country.
The crisis also led to a 54 percent cut to the government's health budget in 2016 from the previous year.
"This malaria crisis is even more dramatic because it is striking an impoverished, hungry population that has no resources and for whom even the slightest shock can have life-or-death consequences," said a diplomat who wished to remain anonymous.
According to WHO, there were 212 million malaria cases in the world in 2015 and 429,000 deaths.