"We are expecting more than 300 [bodies] by the time all the places have been checked," he said.
He did not say how many of the dead were Lou Nuer and how many from the Murle attackers.
In one of the 16 villages razed in the attack, many children drowned in a river as they tried to flee gunmen, he said.
David Gressly, the co-ordinator for the United Nations Mission in Sudan, said that the UN team dispatched to the hard-to-reach area would assess security and humanitarian needs following the violence.
"This time they targeted human beings, not cattle ...They were shooting indiscriminately"
Doyak Chol, commissioner of Akobo county
A smaller, initial assessment team was sent on Sunday but was not able to verify the death toll, he added.
The remote and marshy Jonglei state - where French oil giant Total holds a massive, mainly unexplored concession - has been hit especially hard by cattle raiding and related killings that have split communities along ethnic lines.
Analysts and officials in the southern government have said that as well as disrupting peace, these clashes could derail planned national elections in 2010 and a referendum on independence for the south in 2011.
In March, at least 453 people, mainly women and children, were killed in Lou Nuer attacks on Murle villages.
Those attacks, in which a large number of cows were stolen, were widely thought to have been in retaliation for the theft of 20,000 Lou cattle in January.