• A South Sudanese army soldier sits in a tree as he takes cover from the sun in the town of Paloch. (AAP)
Fighting has returned to South Sudan’s capital after a pay dispute with soldiers led to five dead.
By
Ilya Gridneff

7 Mar 2014 - 6:18 PM  UPDATED 7 Mar 2014 - 6:18 PM

Fighting has returned to South Sudan’s capital after a pay dispute with soldiers led to five dead and fierce fighting in the same barracks that sparked three months of war between pro and anti-government forces.

Late on Wednesday night gunfire and arterially were heard in parts of Juba despite the government and an army spokesman telling media earlier in the day the fighting was contained and the city was under control.

A spokesman for the South Sudan military, Brig. Gen. Malaak Ayuen, said soldiers from the commando division who had not been paid since January went to a commander to demand their salary. The dispute escalated with the commander’s bodyguards and five troops were killed and several wounded.

“This is purely an issue of salaries, it is not political and will not spread, soldiers have not been paid, why I don’t know,” he said. 

Despite the government regaining control of the barracks on-going gunfire and explosions could be heard throughout the capital on Wednesday. 

“This is because the ammo store has caught fire during the clashes,” he said.

All day heavily armed soldiers were quickly ferried around the city on the backs of truck and shops closed out of fear. The U.S. embassy recommended its citizens stay inside while most NGOs sent their staff home.

Juba remains tense with the increased military presence and new roadblocks across the city. The fighting renewed fears for the world’s newest nation, that gained independence from Sudan in July 2011, that despite peace talks hostilities remain deeply rooted.

Ayuen said soldiers are not happy with the way the government has handled the return of many soldiers who defected in December.

“They have been told to forgive and welcome soldiers that have killed their colleagues only a couple of months ago. Now they are back amongst their ranks, it’s too early to forget this” he said.

“The situation is fragile because of the tensions within the ranks,” he said.

On December 15 violence broke out in Juba after a dispute among the presidential guard. That dispute soon pitted backers of the president Salva Kiir against Riek Machar, the former vice president, who now commands the loyalty of a large number of rebel troops who control significant parts of the country. The fighting is perceived as Nuer tribesmen who support Machar, and were the majority of the army, against Kiir's Dinka tribe who held key government roles and top military spots.

The United Nations, that has ranked the crisis on the same emergency level as the Syrian civil war, has reported atrocities and human rights violations by both sides in fighting that has killed many thousands, forced 800,000 to flee their home and put 3.2 million in the immediate need of food.

Toby Lanzer, the U.N.'s humanitarian coordinator in South Sudan, fears if people are too afraid to plant crops there is the potential for famine in the country. The coming of South Sudan's rainy season in two months adds another potential to further worsen the humanitarian crisis as parts of the country become inaccessible.

According to Lanzer,  the U.N priority is now focusing on saving lives, preparing food distribution and "preventing a famine."

The fighting in Juba took most by surprise as the government and the U.N. have been preparing for an assault on oil fields about 150km north on Malakal in the oil-rich Upper Nile state. On February 21 rebels retook Malakal and continue to hold what has become a ghost town littered with dead bodies and destroyed buildings.

Fighting has shut down oil production in Unity state and significantly reduced it in Upper Nile causing serious economic problems for South Sudan, that relies on oil export to mostly Asian partners for 98 per cent of its income.

But while pockets of fighting erupts across the country, South Sudan’s Information Minister Michael Makuei Lueth on Wednesday issued a warning that journalists reporting rebel claims or interviewing Machar would be arrested for “disseminating poison.”

“If you want to do this you will be dealt with, it is agitating and hostile towards the government of South Sudan,you will be dealt with,” he said. 

A local radio journalist has been detained and since fighting broke out in December at least two foreign journalists have been kicked out of South Sudan for a perceived anti-government stance.