The U.N. refugee agency says the conflict was a continuation of fighting that started in August in a village in Upper Nile, and has since spread to other parts of the state and areas of Jonglei and Unity states.
"These killings, along with reports of gender-based violence, abductions, destruction of property and looting, are severe human rights violations and abuses and must stop," U.N. human rights chief Volker Turk said in a statement.
"It is important that the government of South Sudan conducts a prompt, thorough and impartial investigation into the violence and brings all those responsible to account in accordance with international law," he said.
The latest bloodshed risks spreading beyond the region, Turk said, unless local authorities and community leaders act quickly to de-escalate tension between the armed groups.
South Sudan's army spokesperson Lul Ruai Koang said the level of violence had started to ease since the military deployed forces to the area, pushing the fighters from rival communities back. He could not say how many soldiers had been sent.
"It is just a matter of time before the situation will be brought under control," Koang said.
The ongoing violence in South Sudan, which split from Sudan in 2011, contributes to an increase in abductions and sales of children, U.N. special rapporteur on trafficking in persons Siobhán Mullally said in a statement.
"Conflict-related sexual violence including trafficking, remains a serious concern," Mullally said.