Army spokesman Nabil Abdallah said the military had ordered a committee to "evaluate the security situation" in the announcement of a new commander for the restive region in Sudan.
The new chief comes a day after eyewitnesses reported that crowds of thousands protested in front of army headquarters in the state capital Damazin, accusing the government of failing to protect them, with the local university suspending work.
On Sunday, demonstrators demanded the resignation of state governor Ahmed al-Omda Badi, with eyewitnesses reporting the crowd "tried to enter the army headquarters" before "setting fire to the state government building."
At least two hundred people were killed in two days of fighting last week, official media said Saturday, after clashes broke out over reported land disputes between members of the Hausa people and rival groups.
The violence follows clashes earlier this year between the same groups in Blue Nile, leaving at least 149 people killed and 65,000 displaced from July to early October, according to the United Nations.
Nearly 600 people have been killed and at least 211,000 forced to flee their homes in inter-communal conflicts across the country since January, according to the UN.