"Gunshots, heavily armed exchange UN House area once again," the UN Mission in South Sudan (UNMISS) said on Twitter, later adding the fighting was "relentless".
Fighting was heard in several other parts of the city throughout the day, including the tinderbox Gudele neighbourhood -- where rebel leader turned vice president Riek Machar is headquartered -- and the central Tongping area near the international airport, with gunfire intensifying and subsiding at different times.
Regional airline Kenya Airways suspended flights to Juba, citing the "uncertain security situation", while the US embassy in Juba warned its citizens to stay indoors.
Sunday's fighting began on the city's western outskirts where both former rebels and government soldiers have bases at the foot of the Jebel Kujur mountain.
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The nearby UN House site is home to roughly 28,000 people previously uprooted by the war and living in flimsy makeshift houses. Aid workers said rounds had landed inside the UN camp, wounding some civilians.
The violence comes a day after the world's youngest country marked its fifth independence anniversary, and is a fresh blow to a peace deal that has failed to end the civil war that broke out in December 2013.
Helicopter gunships and tanks were also deployed, with a spokesman for Machar saying they were being used to bombard his leader's base.
"Our forces have been attacked at Jebel base," said Machar's spokesman, James Gatdet Dak. "We hope it will not escalate.