Juba was rocked by heavy gunfire late yesterday, with exchanges of automatic and heavy weapons fire heard coming from a district in the south of the city before calm returned in the early hours of the morning.
There was speculation that another army unit had defected to the rebels, although army spokesman Philip Aguer told AFP that the government was "investigating exactly what happened" during the night.
A police spokesman said the fighting may have been caused by "criminals trying to scare people so they can go into houses and steal".
After a terrifying night sheltering in their homes, more residents could be seen trying to get transport south to Uganda, adding to the nearly 200,000 people who have already been displaced by the three-week-old conflict.
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The conflict erupted on December 15, pitting army units loyal to President Salva Kiir against a loose alliance of ethnic militia forces and mutinous army commanders nominally headed by his rival, former vice president Riek Machar.
Kiir has accused Machar of starting the unrest by attempting a coup, although Machar denies this and in turn accuses the president of conducting a violent purge of his rivals.
Fighting has spread across the world's youngest nation, with the rebels seizing several areas in the oil-rich north.
Fighting was reportedly continuing today in Bor, a rebel-held town north of Juba, while clashes were also reported to have broken out during the night in Yei to the south.
The conflict has already left thousands dead, according to UN officials, with both sides alleged to have committed atrocities.