JUBA South Sudan officials said on Tuesday an army patrol might have shot dead 11 civilians, days after the United Nations said the military had killed 10 protesters in a separate incident.
There were varied accounts of what had happened near the town of Gumuruk in Pibor county, Jonglei state.
"The (initial) information I have is that on December 4 the SPLA were patrolling the road from Gumuruk. Near the mountain they were ambushed and they fought. One soldier was injured and 11 rebels were killed. Two guns were recovered," Jonglei governor Kuol Manyang told Reuters.
"Now the information I have from (the federal government in the capital) Juba is that they were civilians," he said. "I spoke to the force commander and he said they were rebels."
Pibor's former human rights commissioner Peter Gazulu said the dead were unarmed civilians rather than members of a local insurgency.
"My brother-in-law was killed there. Also a young boy related to my wife was killed," Gazulu told Reuters.
Pibor commissioner Joseph Konyi told Reuters the death toll was 13.
"According to the army they were ambushed by the rebels. But locals said (those killed) were civilians. We don't know which is true," Konyi told Reuters.
Human rights groups regularly accuse South Sudan's army, a collection of poorly-trained former guerrilla fighters, of human rights abuses.
The army shot dead 10 protesters in another part of the new African country over the weekend, the United Nations said on Sunday.
South Sudan won independence from Sudan last year but its government has struggled to set up state institutions and assert control over vast territories where many people have weapons after decades of civil war with Khartoum that ended in 2005.
In Jonglei a cycle of revenge killings between the Murle and Lou Nuer tribes and a heavy-handed government disarmament campaign have eroded hopes that independence would bring peace.
It also threatens government plans to explore a vast oil concession in Jonglei with the help of France's Total and other foreign oil firms.
The army was not available to comment on the Gumuruk incident despite repeated attempts to reach its spokesmen. The government has played down accusations by rights groups that its security forces committed abuses against civilians during a campaign to disarm civilians and end cattle raiding.
Human rights groups accuse the army of fuelling dissent by committing abuses including rape and torture when it launched the disarmament of the Murle and Lou Nuer early this year in an effort to end bloodshed between the two groups.
The army denies the charges. Many Murle resisted disarmament and fled into the bush where they joined an insurgency run by David Yau Yau, a former theology student, residents in Jonglei say.
A shortwave radio station with links to the Yau Yau rebellion said the group was fighting the government in reaction to abuses committed during the disarmament program.
Nearly 900 people died when about 7,000 armed youths of the Lou Nuer attacked Murle villages in the Pibor area at the end of last year, according to the United Nations.
(Reporting by Hereward Holland; Editing by Ulf Laessing and Andrew Roche)