At least five soldiers have died after heavy fighting broke out in the main military barracks in South Sudan's capital Juba over a pay dispute.
On Wednesday morning, gunfire lasting two hours was heard coming from the barracks, near Juba University, of the presidential guards and other elite troops.
The government played down reports the violence was over a "misunderstanding" about pay.
The army spokesman, Malak Ayuen, told the AFP news agency that five soldiers had been killed and that those found responsible would face a court martial.
"It's unfortunate that this morning fighting ensued among the commandos themselves over salary," he said. "What happened was a misunderstanding among the commandos and it ended in their unit."
According to independent Tamazuj radio, the fighting started after soldiers argued with a military pay committee, which refused to hand over salaries to those not on a list. The station reported that dozens had been killed.
Other local media carried unconfirmed reports that the fighting broke out between guards loyal to the president, Salva Kiir, and a commando unit commanded by top general Gatwech Gai, who had been placed under arrest.
The US embassy in Juba issued a statement advising people to stay indoors as hundreds of terrified residents flooded the main church in Juba, fearing a major outbreak of violence.
"When the fighting started we immediately ran to the church for protection," said Annet Sitima, a local woman.
The conflict in South Sudan started in the capital Juba under similar circumstances nearly three months ago amid tensions within the ruling party between Kiir and the former vice-president, Riek Machar.
The December 15 clashes, which split the army along ethnic lines, spread across the country. The rebels denied any involvement in the latest clashes.
Since the initial week of fighting in Juba, the capital has been largely calm and key installations have been guarded by Ugandan troops, who intervened in the conflict in support of Kiir.
Fighting between the national army and the rebels - made up of defectors and ethnic militia - has centred around the towns of Bor, Malakal and Bentiu further north.
The unrest in South Sudan, the world's newest nation which won independence from Khartoum in 2011, has left thousands dead and has displaced close to 900,000 people, including tens of thousands who have crammed into UN bases fearing ethnic attacks.
The government and rebels signed a ceasefire on January 23, but the truce has seen frequent violations - including a rebel assault on Malakal. Negotiators in neighbouring Ethiopia are trying to broker peacetalks between the warring sides.
The UN humanitarian coordinator for South Sudan, Tony Lanzer, told the Associated Press that refugees were so desperate they were fleeing to Darfur, which is itself in stricken by violence.