President Salva Kiir and his deputy, former rebel leader Riek Machar, were both at the compound preparing to address the media when sporadic gunfire and artillery was heard outside for around 30 minutes.
There was confusion as the shooting died down, with Kiir telling reporters: "What is happening outside is something we cannot explain to you."
The fresh violence came a day after five soldiers were killed in a shootout with former rebels in Juba, just as the country prepares to mark its fifth anniversary of independence from Sudan tomorrow.
Army spokesman Lul Ruai Koang said the five soldiers, all loyal to Kiir, were killed and two others wounded in the shootout at a checkpoint in the city's Gudele neighbourhood.
Gudele was the scene of tribal massacres at the outbreak of the war in December 2013.
A UN worker was also reportedly injured in a separate shooting and a US embassy vehicle was also shot at, according to Nyarji Roman, a spokesman for rebel leader turned vice president Machar.
Fighting has continued outside the capital with the most recent serious clashes taking place in the town of Wau late last month.
The peace deal was supposed to end a civil war that began when Kiir accused Machar of plotting a coup.
But Machar did not return to the capital until April, and fighting has continued despite the establishment of a unity government.
Roman said yesterday's shooting began when two vehicles used by Machar's bodyguards were stopped by soldiers. He said two former rebels were also injured in the clash.
Tens of thousands of people have died in more than two years of civil war, close to three million have been forced from their homes and nearly five million survive on emergency food rations.
The country is also facing an economic crisis with the currency collapsing and inflation spiralling out of control.
South Sudan's mainstay oil industry is in tatters and regional towns have been razed.
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