Fighting broke out Sunday between the Hausa and Nuba ethnic groups in Kosti, the capital of White Nile state which borders South Sudan, local media reported.
The violence was seen as unrelated to major military clashes that have flared across Sudan since April 15 between forces loyal to two rival generals which have claimed at least 750 lives.
Tensions have long simmered between the ethnic groups -- centred on disputes over scare water and land resources between farmers and pastoralists -- and have often flared into deadly violence.
It was not immediately clear what triggered the latest clashes in White Nile, which media said had "killed 16 people on both sides, wounded large numbers, and left some houses burnt".
The Sudanese Hausa, part of a larger African ethnic group, charge they are discriminated against by being treated as outsiders and barred from owning land in Blue Nile.
Between July and early October last year, at least 149 people were killed and 65,000 displaced in Blue Nile, according to the United Nations.
Access to land often fuels tensions in the arid and impoverished country, where farming and herding account for 43 percent of employment and 30 percent of GDP according to UN and World Bank data.
Sudan as a whole has been gripped by wider chaos since a power struggle exploded into violence between forces loyal to army chief Abdel Fattah al-Burhan and his former deputy Mohamed Hamdan Dagalo, who commands the paramilitary Rapid Support Forces.
The fighting in the capital Khartoum and other cities has so far killed 750 people, wounded thousands and uprooted hundreds of thousands, with many refugees fleeing the country.