Yet-to-be identified attackers wearing civilian clothing hit two military installations in Bujumbura, and one in the countryside marking a rise in simmering conflict.
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The attacks in the early hours of Friday led to clashes with troops that left at least 12 fighters dead, an army spokesman said.
Residents said some of the dead had been rounded up by the police during the day after house-to-house searches on Friday, an allegation the police denied.
The outbreak of violence is unnerving for a volatile region which only two decades ago saw a genocide in next-door Rwanda. Several hundred people have also been imprisoned for opposing Nkurunziza’s re-election this year.
A neighbor said he heard the police coming down the street and banging on doors, shouting that they knew that guys who had used grenades against them lived there. Many terrified civilians in Bujumbura stayed in their homes.
Gaspard Baratuza told state radio that 20 other fighters were arrested after the attacks on a base at Ngagara in the north of Bujumbura and a military training college in the south.
A source in the presidency said a declaration of a state of emergency was under consideration.
Willy Nyamitwe, a presidential media adviser, using a term to describe political opponents, tweeted: “Situation is returning to normal as firearms are seized, many Sindumuja assailants killed or arrested”.
In a statement Monday, U.S. National Security Council spokesman Ned Price called for all sides in Burundi to reject violence and take part in an internationally mediated dialogue, outside the country, to resolve the crisis.
Baratuza said five soldiers were wounded in the strikes. At least 240 people have been killed since April and about 215,000 have fled to neighbouring countries, according to the UN.
Kenya Airways, RwandAir and Ethiopian Airlines all cancelled their flights to Burundi.
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One of the generals behind the failed coup attempt in May said in July the rebel group still aimed to topple the president and experts have warned that the army, which was restructured after the civil war to include rebel fighters, might fracture.
