"There have been mass killings, a massacre," said Joshua Konyi, commissioner for Pibor county in Jonglei state.
"We have been out counting the bodies, and we calculate so far that 2,182 women and children were killed and 959 men died."
United Nations and South Sudanese army officials have yet to confirm the death tolls and the claims from the remote region could not be independently verified.
If confirmed, the killings of 3,141 people would be the worst outbreak of ethnic violence ever seen in the fledgling nation, which split from Sudan in July.
A column of some 6,000 rampaging armed youths from the Lou Nuer tribe last week marched on the remote town of Pibor, home to the rival Murle people, whom they blame for abductions and cattle raiding and have vowed to exterminate.
The Lou Nuer gunmen attacked Pibor at the weekend, torching huts and looting a hospital, and only withdrew after government troops opened fire.
Over a thousand children are missing, feared abducted, while tens of thousands of cows were stolen, added Konyi, who comes from the Murle ethnic group.
The UN humanitarian coordinator for South Sudan, Lise Grande, said earlier this week that she feared "tens, perhaps hundreds" could have died.
"Yes, there have been casualties, but we don't have the details, and can't at present confirm what the commissioner reports," said Jonglei state information minister Isaac Ajiba.
"We are awaiting reports from our (military) forces on the ground," said South Sudan army spokesman Philip Aguer. "For the assessment to be credible they must have gone into the villages to count all the bodies."
South Sudan has declared Jonglei state a national "disaster area" according to the official government website, while the UN has warned a "massive emergency operation" is needed to help those uprooted by the violence.
Both ethnic groups must "return all the abducted women and children of both sides and reunite them with their communities," the government added.
Lou Nuer fighters are now returning homewards, after the army and UN peacekeepers beefed up reinforcements in Pibor, while the World Food Programme (WFP) has flown in emergency rations to support the thousands displaced.
Doctors Without Borders (MSF - Medecins Sans Frontieres), the main healthcare provider for the estimated 160,000 people in Pibor county, has temporarily suspended its operations after the clashes forced them to evacuate staff.
Newly independent South Sudan was left in ruins by decades of war with northern Sudanese forces, who fuelled conflict by backing proxy militia forces across the south, often exacerbating historical enmities between rival groups.
Ethnic violence, cattle raids and reprisal attacks in the vast eastern state left over 1,100 people dead and forced some 63,000 from their homes last year, according to UN reports based on local authorities and assessment teams.
The deaths include violence last August, when at least 600 people were killed and up to 985 people injured after Murle gunmen attacked Lou Nuer villages in Jonglei.