Medical sources told Reuters those killed included women and children, with signs of bullet wounds, burning, and stabbing.
Earlier this week, violence had flared in another southern province, West Kordofan, following a tribal dispute over land.
The Sudanese military accused the rebel group led by Abdelaziz al-Hilu, who did not sign the agreement, of exacerbating the conflict, while his group in a statement accused the paramilitary Rapid Support Forces.
The violence erurpted again on Oct. 13, with fighting involving the Hausa and Hamaj tribes in addition to others in the Wad Almahi area over several days, the U.N. said in a Thursday statement.
The U.N. said that at least 36,500 had fled Lagowa, the site of the violence, and that 19 were killed and 34 injured.
"Sustainable peace won't be possible without a fully functional credible government that prioritizes local communities' needs including security [and] addresses the root causes of conflict," the U.N.'s special mission said in a tweet commenting on the incidents in both states.