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President Salva Kiir and his vice president, former rebel leader Riek Machar, were both preparing to address the media at the government compound when artillery fire erupted outside. The two leaders, who had met to discuss a fragile peace deal, told reporters they did not know what was happening.
Kiir and Machar called for calm on Friday at the State House. South Sudanese radio urged citizens to stay at home.
Fighting nevertheless continued Friday night outside a UN building sheltering around 28,000 displaced people in Juba, with UN staff reporting heavy artillery coming from “all around” the base.
The UN mission in South Sudan tweeted “heavy gunfire+shelling” at its civilian protection site.
A doctor in Juba said on Saturday that soldiers had brought in scores of bodies from Friday’s gun battles.
The doctor told AP that a death count was not available because soldiers are not allowing medical staff to examine the bodies, but he said the morgue is full at Juba Teaching Hospital.
UN chief Ban Ki-moon said he was deeply alarmed by the fighting, calling the gunbattles between rival troops a “new betrayal” of the country’s people.
“[The fighting] represents a new betrayal of the people of South Sudan, who have suffered from unfathomable atrocities since December 2013,” the UN chief said in a statement.
“I am also gravely concerned by the resurgence of violence in Wau and Bentiu, which could lead to a dramatic deterioration of the security situation across the country,” the UN chief said.
The gunfire came a day after five South Sudanese government soldiers were killed in a shootout between opposing army factions in Juba.
The deadly clash reportedly started when a group of soldiers backing Kiir stopped vehicles carrying Machar loyalists in Gudele, a district of Juba where Machar has his political base.
A spokesman for the opposition SPLA-IO, Colonel William Gatijiath Deng, told Reuters the fighting began after Machar’s forces refused to allow their vehicles to be searched.
The violence is similar to the skirmish between soldiers in the capital in December 2013 that led to the country’s civil war, in which tens of thousands of people were killed.
It was the first violent flare up in Juba since Machar returned in April, under a deal to end two years of civil war. Ban described the fighting as “yet another illustration of the parties’ lack of serious commitment to the peace process.”
Experts have warned that the five-year-old nation risks sliding back into conflict unless the two sides move more swiftly to implement the peace pact, including ensuring the swift re-integration or demobilisation of rival combatants.