Fighting broke out Thursday along the de facto border between North and South Sudan after fighters loyal to Sudanese militia leader Gabriel Tang refused to surrender their weapons.
Described as mutiny by members of the Joint Integrated Units of Sudan's military, the fighting left as many as 50 dead, CNN international reports.
Maj. Gen. Ahmad al-No, a spokesman for a joint military defense council in Sudan, told CNN the militia leader may create problems in Sudan's south.
"I am concerned that he may have and affect on the security in the region," he said, adding Tang was loyal to neither governments.
The conflict comes as results from a referendum for an independent South Sudan passed with overwhelming support.
The January vote for an independent South Sudan was part of a 2005 peace agreement that ended the civil war between the north and south.
Sudanese President Omar al-Bashir said on state television Monday that he would honor the vote but stressed his commitment to maintaining ties to the government in Juba, al-Jazeera reports.
"Today we received these results and we accept and welcome these results because they represent the will of the southern people," the Sudanese president was quoted as saying.