Thousands have been killed and an estimated half million have fled fighting in South Sudan, pitting the government of President Salva Kiir, an ethnic Dinka, against former Vice President and rebel leader Riek Machar, an ethnic Nuer.

In recent days government forces, supported by Ugandan troops, apparently wrested two key towns, Bor and Malakal (both important to the oil industry) from the control of rebels. Yet despite initial hopes, there are signs that a quick peace may be further away, not closer, in the world’s newest nation. One reason is a lack of command and control over an ill-disciplined military that may be reverting to its roots as a militia.

The Sudan People’s Liberation Army (SPLA), the core military force, is a sprawling patchwork of local commanders who at times fought each other, as well as the government of Khartoum, during decades of insurgency. South Sudan’s leadership rivalry has led commanders and their patronage networks into shifting alliances between President Salva Kiir and rebel leader and former vice-president Riek Machar, according to analysts.

Even if Mr. Kiir and Mr. Machar agree to a ceasefire – and so far Machar has not even shown up at talks in Addis Ababa — they may struggle to enforce it. The risk is that unit commanders will form and disband alliances as the opportunity dictates, underlining the failure of politicians like Kiir to forge a unified army.

Diplomats in Addis Ababa are still worried about a full-blown, prolonged civil war as the SPLA and rebels strive for a clear battlefield victory at the expense of the peace talks here.

Harry Verhoeven, an expert in African Politics from Oxford University says that both leaders “continue to believe in all-out military victory,” and that Kiir, with Uganda’s support, has an advantage and can “go for broke … a move that risks starting a wider regional escalation of the conflict.”

The conflict research group Small Arms Survey warns that if South Sudan’s government controls major towns while opposition forces roam the countryside, fighting could prove to be “interminable.”

The current crisis began last month as a power struggle between Kiir and Machar, but quickly took on a brutal ethnic or tribal character, dividing neighbors and friends across the country’s north and east.

The deep-seated rivalry between the two rebels-turned-politicians stems partly from their presidential ambitions – an election is due in 2015 – and the determination to control the movement that liberated the new nation. Both men are more accustomed to leading troops than politicking.

To get the peace talks in Addis Ababa started, Machar called on Kiir to release 11 prisoners accused of helping to plot a coup in December, and he faces Western pressure to release them as well. During the peace talks, Kiir has also turned to Uganda for military support that would allow him to prolong a fight for territory and leverage.

Despite the SPLA’s retaking of Bor and Malakal this week, the rebels vow to continue. “We are still in control of rural areas,” Brig.Gen. Lul Ruai Koang of the rebels said Monday. “These [government] people are more or less surrounded. They are trapped.”

Retinue of generals

Alex de Waal at Tufts University says that little has been done to build structure and coherence in South Sudan’s military since 2005 when war ended with the North, exacerbating the difficulty of hammering out a peace deal to end the current crisis.

“Most of the army is the retinue of generals. It has no real command and control,” Mr. de Waal says. “Most of it is entirely chaotic.”

The West has backed security reform in South Sudan, including three attempts to create a national payroll for soldiers. But this plan has not gained traction and plans to shrink the Army – which takes up half the country’s budget, mostly in salaries – have floundered.

De Waal says a peace deal or ceasefire may not be seen as advantageous within the Army: “Is any of it going to be implemented while you have 200,000 men under arms who are demanding their piece of the patrimony at gunpoint?”

Bad blood between Kiir and Machar stretches back to the decades-long insurgency against the north, which culminated in the South’s secession in 2011.

Kiir, a member of the large Dinka group, was second-in-command to revered leader John Garang of the main rebel army, called SPLA. Machar left the SPLA and allied himself with the Khartoum government, and in 1991 led Nuer forces to massacre thousands of Dinka in Bor.

Later, Machar set up his own rebel outfit against the north before finally rejoining the SPLA as a senior commander. His complicated journey towards reintegration is shared by other fighters who joined the SPLA in exchange for a high rank and cut of the country’s oil wealth.

“The late John Garang described running the SPLA as ‘reforming the mob,’ but he didn’t have much success at the reform, and neither has his successor,” says de Waal. “It is still a mob, and no-one has a good idea how to reform it.”

A lull in fighting may take place if rebels run out of ammunition and do not find an external backer, says Jonah Leff, South Sudan expert for the Small Arms Survey. But Mr. Leff says the rebels can end up buying bullets “at any border, really.”

The real solution he argues is a political settlement that addresses security sector reform, disarmament, and the military’s size and ethnic makeup – but that this will “take a very long time.”