A statement from the presidency confirmed that Lual Akook Wol Kiir, a "distant cousin" of the president, had been arrested and was in hospital in critical condition after the incident.

The army said the incident in the Shirkat area of Juba was sparked by a land dispute, the details of which are not clear.

"Lual is trying to grab land from the civilians. And when the citizens tried to reopen their businesses Lual came with his soldiers and immediately started shooting civilians," said an eyewitness, Malual Peter.

Army spokesman Major General Lul Ruai Koang told AFP there had been "a misunderstanding ... it got out of hand and as a result some shooting ensued between him (Lual) and his bodyguards on one hand and civilians on the other."

He said the bodyguards are still at large.

Four men and one woman were killed, the statement from the presidency said.

"The president condemns this in the strongest terms possible and has directed authorities to investigate the incident and press charges ... immediately," it said.

The killings prompted a rare anti-government protest as hundreds called for the president to step down, holding up handwritten placards reading: "Kiir must go", and "We don't want killer regime" while singing "down, down Salva Kiir".

Koang said the situation had been brought under control after security forces were deployed.

"Things grew sharply after some civilians were killed and some civilians attempted to cause some insecurity and therefore we have deployed some security forces for law and order to be maintained," he said.

Kiir has been president since South Sudan achieved independence in 2011, overseeing a brutal civil war which started in 2013.

Fighting between government forces and the main rebel groups ended with the signing of a peace deal in September 2018 and the formation of a unity government in February, however clashes with some holdout rebels have continued.

Both government troops and rebel forces have been accused of numerous atrocities against civilians in South Sudan, and examples of justice are extremely rare.