Another 57 people were wounded, three of whom were soldiers, the army said.
“Houses were damaged in various neighbourhoods as well as private vehicles. Military equipment and facilities burned and were destroyed,” army spokesperson General Gaspard Baratuza added in the latest update.
The explosions erupted late on Tuesday at the main ammunition depot of the Burundi National Defence Force (FDNB) in Musaga, a southern suburb of Bujumbura.
The army confirmed on Wednesday that 13 civilians had been killed, without specifying if any soldiers died in the incident. Earlier, security sources had told AFP that dozens of people had been killed.
An army spokesman had said the cause was an “electrical accident”.
In videos seen by AFP, clouds of smoke loomed over the neighbourhood during the blast, sending panic through the city of more than a million people.
Earlier Wednesday, a high-ranking army officer told AFP: “It is impossible to establish a toll for the moment, but dozens and dozens of people have been killed, and there are hundreds or even thousands of injured.”
A senior police officer present at the site said the detonation broke out “where heavy weapons and ammunitions are stored, which is why we immediately heard large explosions”.
“There are dozens of dead, but the toll may be higher,” the senior police officer said.
Prisoners among dead
The arsenal in Musaga is located in a densely populated area and adjoins the Higher Institute for Military Cadres (ISCAM), where aspiring army officers are trained and housed.
It also houses numerous army logistics depots and is next to another military base, Muha camp, and the central Mpimba prison.
A source at Mpimba prison told AFP that eight inmates had been killed and several others injured, who were taken to hospital by the Red Cross early Wednesday.
With the authorities still to provide a definitive summary of the casualties figures, one Western diplomat speaking to AFP on condition of anonymity expressed doubt that “there will be transparent communication”.
“The regime here is very reluctant to communicate about deaths, especially military ones,” he added.
Burundi, ranked by the World Bank as the world’s poorest country by GDP per capita in 2023, has faced years of deep economic crises. The most recent saw a severe fuel shortage that has paralysed the nation for the past three years.
‘Massive inferno’
Spageon Ngabo, director of the online bloggers’ platform Yaga Burundi, said around 10 deaths had been reported by citizens to his organisation.
“We haven’t finished counting yet,” Ngabo said.
The senior police officer, who joined the firefighting team late Tuesday, said efforts were immediately slowed by a water shortage.
He said property had been destroyed by the “massive inferno” and that the “base camp was reduced to ashes”.
On Wednesday afternoon, fire and smoke could still be seen, according to the police officer.
Residents in surrounding neighbourhoods fled their homes at night, the officer said, as fire-triggered projectiles landed nearby.
A witness speaking to AFP called the scenes “horrible”, adding that a projectile had torn through a neighbour’s bedroom, killing him.
President Evariste Ndayishimiye, in a message on X, expressed his “sympathy” to “all those who have been victims of the fire”.
Burundian authorities have urged citizens to report unexploded munitions by phone, warning: “Be careful and DO NOT TOUCH.”
On social media, dozens of posts showed children being searched for by parents who lost track of them while fleeing.