Ethiopian police have launched investigations to trace the governor of Gambella region, government officials have said.
Okelo Okuaye disappeared on Friday with his bodyguards, the region's police commissioner Kongo Lule said.
Gambella region was the scene of bitter clashes between ethnic Agnwak and Nuer last December in which at least 57 people were killed.
Opposition sources say Mr Okuaye has fled to Sudan after a row with a government official over how many people died in the clashes and who was responsible.
But a government spokesman told the BBC's Mohammed Adow in Ethiopia, that Mr Okuaye had no reservations about the official figures.
Our correspondent says that although up to 5,000 Ethiopian troops have helped restore calm, tensions remain high in the region, where many different ethnic groups compete for land.
The violence was sparked by an attack on a United Nations vehicle in early December.
Eight people in the vehicle, including three government refugee workers were killed. Their bodies were said to be badly mutilated.
A radical Agnwak group was blamed for the attack, which occurred as the government officials travelled to Odier, a proposed new camp for Nuer and Dinka refugees from Sudan.
The reprisals that followed against the alleged perpetrators were ferocious.
Hundreds of homes were burnt down and the killings continued for several days.