This is raising fears of a broader civil conflict in the two-year-old nation.
An official in Bor, north of Juba, said soldiers attacked each other at two military barracks and one journalist said troops loyal to Vice President Riek Machar now controlled them, suggesting violence was increasingly running along ethnic lines.
Soldiers in the capital Juba have clashed since Sunday, killing up to 500 people, in what President Salva Kiir said was an attempted coup launched by Machar's supporters.
The president sacked Machar in July and political tensions have simmered since then in the oil producing nation.
According to the online journal Sudan Tribune, Machar denied any role in the fighting or any coup attempt.
In Bor, where Nuer soldiers loyal to Machar in 1991 massacred hundreds of Dinka, the ethnic group of Kiir, the locals feared the fighting could spill beyond the barracks.
"Last night there was fighting in two military barracks," Hussein Maar, deputy governor of Jonglei state, told Reuters, although he said the town of Bor was calm.
A journalist in Bor told Reuters by telephone that troops led by Commander Peter Gadet, a Machar ally, had taken control of the bases, abandoned by the outnumbered Dinka soldiers. But details were sketchy and according to another account only one base was in the hands of Machar's allies.
The United Nations in South Sudan reported fighting on Wednesday morning in Bor area, saying on its Twitter feed that more than 1,000 civilians sought refuge in the U.N. compound.
A broader conflict could threaten vital aid and be exploited by neighbouring Sudan, which has had persistent rows with Juba over their undefined borders, oil and security. That would further hurt efforts to build a functioning state in the south.
In Juba, residents reported a tense calm after sporadic gunfire overnight, with traffic returning to the streets.
But the US State Department said it was organising evacuation flights and Britain said it was gathering the names of any citizens who wanted to leave. Other Western nations were expected to follow. Many aid workers live and work in Juba.
The government said it arrested 10 people, including seven former ministers, over the "foiled coup" and wanted to question several others, including Machar.
Diplomats said the United Nations had reports of between 400 and 500 people killed and up to 800 wounded in the nation that declared independence in 2011 from Sudan, after decades of civil conflict that left the south with barely any tarmac roads.
"Most people are scared they might be confronted with a mob or see dead bodies," said one aid worker in Juba, adding that the city was calmer on Wednesday morning, after residents awoke to heavy gunfire and artillery blasts on Monday and Tuesday.
Political tensions have been mounting since Machar's dismissal. The former vice president has said he would run for president and has accused Kiir of being dictatorial.
Kiir had said before the clashes that his rivals were reviving rifts that provoked infighting in the 1990s. He has faced public criticism for doing little to improve life in one of Africa's poorest nations.
"Salva must recognise that the charge of his being 'dictatorial' has taken deep hold, and he must do what is necessary to shed the label as much as possible," South Sudan expert Eric Reeves wrote in an assessment of the violence.