The violence in the two states is some of the most significant fighting reported since the signing of a peace agreement in October, which observers hoped would end years of war.
While former rebel forces have committed to lay down their weapons, decades of conflict have left the vast western region awash with weapons and divided by bitter rivalries.
Key issues include land ownership and access to water.
It also comes just over two weeks since the hybrid United Nations African Union Mission in Darfur (UNAMID) ended operations in their long-running peacekeeping mission.
“The clashes between the Rizeigat tribe and the Fallata tribe have stopped, and we have now counted 47 deaths,” local leader Mohamed Saleh told AFP.
Saleh, from the ethnically non-Arab Fallata people, added that several houses were burned in the attack.
The violence – which erupted early Monday – came after the killing of at least 83 people in clashes between rival ethnic groups on Saturday and Sunday in Sudan’s West Darfur state.
Sudan has been undergoing a fragile transition since the April 2019 ouster of president Omar al-Bashir following mass protests against his rule.
The civilian-majority administration installed after Bashir’s ouster has been pushing to stabilise regions beset by decades of civil war.
Darfur endured a bitter conflict that erupted in 2003, leaving roughly 300,000 people dead and 2.5 million displaced, according to the UN.
The main conflict has subsided over the years but ethnic and tribal clashes still flare periodically, largely pitting nomadic Arab pastoralists against settled farmers from non-Arab ethnic groups.
Only two groups refrained from signing the peace deal, including one with considerable support in Darfur.
The UNAMID peacekeeping force plans a phased withdrawal of its approximately 8,000 armed and civilian personnel within six months.