At least 45 people have died in fighting between ethnic groups in South Sudan's northern state of Western Lakes, a local official said, in a new source of violence in a country already devastated by a four-year civil war.

Shadrack Bol Maachok, the state's information minister, said the clashes in Malek county started after a group of young people from the Ruop ethnic group attacked rival youth from the Pakam tribe on Wednesday and Thursday.

Early on Friday, the Pakam fighters launched a revenge assault on the Ruop, with the fighting still raging late into the day.

"It was a very heavy fighting, it has left more than 45 people dead and many injured," he said.

The death toll is likely to climb as the area is remote and officials are still trying to gather information on the incident, he said.

In the clashes, houses were burned down and properties destroyed, Maachok said, adding that South Sudan's military, SPLA, had deployed troops from the state capital Rumbek to try to stop the violence.

The UN mission in South Sudan UNMISS estimated the death toll at more than 50 and said it had dispatched a military patrol to the area to establish the level of destruction and the impact on civilians.

"We hope to engage the leaders of the fighting parties to press the need to refrain from revenge attacks. We will also intensify patrols to deter further violence," UNMISS said.

South Sudan was plunged into war in 2013 after a political disagreement between President Salva Kiir and his former vice president Riek Machar escalated into a military confrontation.

The fighting has killed tens of thousands, uprooted about a quarter of the country's population of 12 million people and left its small, oil-dependant economy moribund.

Violence between rival communities is common in parts of South Sudan, often triggered by quarrels over scarce grazing land and cultural and political grievances. But the death toll is rarely large.

The minister said this week's skirmishes stemmed from disputes dating back to 2013 but it was not clear what exactly sparked the grievances.