Some 16,000 people have fled ethnic clashes in Ethiopia for Sudan over the past month, according to the World Relief aid agency.
Gambella is home to many ethnic groups, who compete for land
The agency's director told the BBC that many ethnic Agnwaks had walked for three days and were now camped in a school and church in Pachala town.
Myron Jesperson said that up to 300 people were arriving every day.
The fighting between Agnwaks and Nuers over land in Ethiopia's Gambella region left at least 57 people dead.
Meanwhile, Ethiopian police are still seeking Gambella's governor, who disappeared on Friday.
Opposition sources say the disappearance of governor Okelo Okuaye is linked to the ethnic clashes.
They say he fled to Sudan after a row with a government official over how many people died in the clashes and who was responsible.
But an Ethiopian 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.