About 400 members of the Beni Amer tribe in Sudan demonstrated in Gedaref town demanding the resignation of the state commissioner and the chief of police, with some of them attacking police vehicles, the witness told AFP, speaking on condition of anonymity.
It was not immediately clear who was responsible for the gunfire or whether there were any casualties.
The protest took place after clashes on Wednesday that erupted when the municipal police tried to implement the orders of the local authorities to remove cow shelters erected by the Beni Amer within the town.
Two civilians were killed and a policeman wounded, according to the interior ministry.
The demonstrators said in a statement obtained by AFP that they would neither negotiate with the government nor hand over the two bodies until the state commissioner and chief of police resigned.
The Beni Amer, who live either side of the Sudanese-Eritrean border, are a branch of the traditionally camel-herding Beja ethnic group, many of whom resent their perceived marginalisation by the Khartoum government.
Large numbers have migrated to the cities in recent years, partly due to a succession of severe droughts in the region and competition for grazing pastures.
The Beja are the largest ethnic minority in resource-rich but neglected eastern Sudan, and fought alongside the Rashidiya Arab tribe in a decade-long rebellion against Khartoum, which ended with a fragile peace agreement in 2006.