Sudan will begin evacuating its nationals from Juba on Friday after fears that fresh fighting could erupt in South Sudan, which split from the north five years ago.

South Sudanese voted for independence from Sudan under a peace agreement in 2011 but the world's newest country fell into a civil war that has killed tens of thousands of people.

Hundreds have died in the latest round of violence that broke out in the South Sudanese capital ahead of the country's independence anniversary last week.

Although a ceasefire has held since late Monday, the United Nations has warned of tension and the possibility of fresh fighting in Juba.

Specially chartered evacuation flights have been taking foreign nationals out of the country since Wednesday.

"The first flight evacuating Sudanese from South Sudan will arrive tomorrow," said a statement issued by Sudan Media Centre, an outlet close to the powerful National Intelligence and Security Service.

"We have registered 2,000 Sudanese who want to return to their homeland," the statement quoted Sudanese government official Hajj Magid Suor as saying.

He said Sudan will operate three to four flights daily to bring home its nationals.

"Most of them are traders and those working in international NGOs. They are in thousands," Suor said.

Commercial flights resumed to the South Sudanese capital on Thursday morning, with planes arriving almost empty and leaving full of people desperate to get out.

Four days of intense battles last week between soldiers loyal to President Salva Kiir and former rebels backing Vice President Riek Machar left hundreds dead in Juba and forced around 40,000 to flee their homes.

Aid agencies are warning of a worsening humanitarian crisis with a lack of both water and food.

But the latest bloodshed had so far not triggered a jump in the number of South Sudanese refugees arriving in Sudan, the UN Office for the Coordination of Humanitarian Affairs, or OCHA, said.

"No substantial increase in the number of arrivals into Sudan has been observed since the eruption of violence in Juba on 8 July," OCHA said.

UN officials say a key reason for this was that the latest fighting was not in areas along the border between the two countries, which otherwise would have led to a jump in refugee influx into Sudan.

Also those South Sudanese who wanted to flee were possibly finding it difficult to travel to Sudan from Juba, a UN official told AFP.

South Sudanese refugees have been entering Sudan since a civil war erupted in their country at the end of 2013.

OCHA said 80,758 South Sudanese arrived in Sudan between January 1, 2016 and July 10, fleeing conflict and food shortages in their war-torn country.

It did not say how many entered the country since the violence erupted in South Sudan.

The majority of new arrivals have taken refuge in East Darfur.

The latest violence marks a fresh blow to last year's deal for ending the conflict, which erupted when Kiir accused Machar of plotting a coup.

Kiir is a member of the Dinka tribe, while Machar is a Nuer, and the dispute has split the country along ethnic lines.

Machar's sacking set off a cycle of retaliatory killings that split the poverty-stricken, landlocked country along ethnic lines.

Tens of thousands of people have been killed and more than two million have been driven from their homes.

The conflict has been characterised by horrific rights abuses, including gang rapes, the wholesale burning of villages and cannibalism.