The clashes occurred on Saturday in South Darfur's camp Kalma, one of the biggest facilities housing thousands of people displaced by the war in the region.
He did not say what triggered the violence or reveal details about the groups that clashed, but said the camp has "lot of weapons and groups that disturb the state's security".
The conflict in Darfur erupted in 2003 when black ethnic rebels took up arms against the Arab-dominated government of now ousted president Omar al-Bashir, accusing it of marginalising the region economically and politically.
Khartoum cracked down on rebels and since then insurgent groups have fragmented, with fighting punctuated by periods of relative calm.
In recent years the level of violence has significantly dropped across Darfur, with Khartoum insisting the conflict has ended in the region.
Tens of thousands of people continue to live in sprawling camps like Kalma.
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