South Sudanese will also vote next January on independence from the north after decades of civil war, and the latest attack highlights an urgent need to demarcate the north-south border and determine the rights of those whose livelihoods traverse the frontier.
"The Misseriya (nomads) have yesterday attacked our forces again," southern army spokesman Kuol Deim Kuol told Reuters on Friday. "They killed two SPLA (southern army) soldiers ... (and) a body from the Misseriya was found."
Four other southern soldiers were also wounded, he said. A similar attack happened in early February on the same army base in oil-producing Unity state close to the north-south border where northern nomads seasonally graze cattle.
In the February gun battle at least 18 people were killed.
East African nations met this week and urged Sudan's north-south former foes to reach agreement on the post-referendum situation within two months as the vote fast approaches.
Citizenship, sharing of Sudan's 500,000 barrels per day of crude oil and a disputed census are some of the post-referendum arrangements yet to be solved.
Southern officials have said that about 70 percent of the border has been agreed upon but that there are still at least four areas of contention including oil-producing areas.
Analysts worry a widely expected vote for independence could cause conflict if the border, which could cut off southern pastures vital to northern pastoralists, is still unclear.
"The south seceding is a threat to their livelihoods and, as the referendum approaches, rising tensions could result in a further loss of life," said Maggie Fick, an analyst from the U.S.-based Enough Project.
The south's semi-autonomous government says the nomads are welcome but must leave weapons in the north, but herders say this leaves them vulnerable to wild animals and cattle raiders.
An agreement signed earlier this month between the herders and southern officials, including from Unity State, says that the nomads may now bring in five small guns to accompany large herds and three guns if they are moving with smaller groups.
"But they (the nomads) are coming with too many guns, they are not implementing this," Kuol said. The agreement also states that the herders are to pay a 5 Sudanese pound ($2.24) levy for each cow grazing in the south, Kuol said.
The attack was probably a result of southern officials trying to stop nomads with large numbers of guns from entering the south and also partly in revenge for those killed in last month's fighting, Kuol said.
Northern nomadic groups were used by Khartoum in the war as proxy fighters against the southern rebels. But in some areas they also formed close trading links with southern communities.
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