"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 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 cattle raiding and have vowed to exterminate.
The Lou Nuer gunmen attacked Pibor and only withdrew after government troops opened fire.
Over a thousand children are missing, feared abducted, while tens of thousands of cows were stolen, Konyi added, 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."
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 in 2011, according to UN reports based on local authorities and assessment teams.