The president, who has been in power for 15 years, was said to have died at a hospital on Monday.
Although the government of Burundi said Nkurunziza died of heart attack, the local media had earlier reported that he had contracted coronavirus.
Taarifa, a Rwandan newspaper, had quoted a source as saying: “Nkurunziza is in the hospital in Karusi suffering from #COVID-19.”
Thierry Uwamahoro,a US-based social commentator who tweets frequently on Burundi issues, also said the president had contracted COVID-19.
In his lifetime, the late president had said there was no COVID-19 in his country, disregarding all measures WHO recommended to check the spread of the disease.
He even encouraged a presidential election in May and Evariste Ndayishimiye, his ally, was declared winner.
Ndayishimiye is expected to take over in August.
Millions of citizens are feared to have been exposed to the disease in course of the elections as safety measures including social distancing and wearing of face masks were disregarded in the process.
Even as the country has a total number of 83 confirmed cases of the disease, 45 recovered patients and one death, the late president did not hide his feeling that his country was free of COVID-19.
“So far, we believe that the situation is looking good. Finally, as we keep repeating, Burundi is an exception among other nations, because it is a country that gave God first place, a God who guards and protects him from all misfortune,” Jean-Claude Karerwa Ndenzako, Nkurunziza’s spokesman, had told BBC before the election.
“It is not the first time that the world has been hit by a calamity, but, each time, Burundi has been spared. We have faith in our God, especially now that in our country we have put God first, he will protect us from all calamity.
“But whether you believe it or not, Burundi is a country that has signed a special pact with God.”