"Sudan's armed forces understand the reasons for the demonstrations and is not against the demands and aspirations of the citizens, but it will not allow the country to fall into chaos," Ibnouf said on Monday, according to the official SUNA news agency.
In a separate statement, army chief of staff Kamal Abdelmarouf said the military was "discharging its responsibility in securing and protecting citizens."
Officials say 38 people have died in protest-related violence since December.
Interior Minister Bushara Juma said seven protesters died and 15 were wounded on Saturday when forces tried to disperse them.
He said 42 security personnel were injured and 2,496 arrests made.
The umbrella group spearheading the protests appealed to the army on Monday for talks on forming a transitional government.
"We call on the Sudanese armed forces to talk directly with the Alliance for Freedom and Change for facilitating the peaceful process of forming a transitional government," said Omar el-Digeir, a senior member of the group.
Digeir said the protest organisers had formed a council to open talks aimed at agreeing a "transitional government that represents the wish of the revolution".Reading from a statement, he also called on the armed forces "to withdraw their support for a regime that has lost its legitimacy" and to support the "people's alternative for a transition to a civilian democratic government".
The rally outside the army headquarters has been the largest since protests began on December 19 in the central town of Atbara, quickly spreading to the capital and nationwide.
The European Union said an "unprecedented" number of people had come out calling for change since Saturday.
"The people of Sudan have shown remarkable resilience in the face of extraordinary obstacles over many years," the EU's External Action Service said.
"Their trust must be won through concrete action by the government."
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