A top Sudanese general has said the new joint civilian-military council will be headed by the current chief of the ruling military council. The move has been denounced by leaders of the protest movement that brought down former strongman Omar al-Bashir.
Demonstrators have already called the military council headed by General Abdel Fattah al-Burhan "a copycat of the toppled regime".
Sudan's generals set up a military council after they toppled veteran president Bashir on 11 April.
They have since resisted protestors calls to step down.
However, in a breakthrough on Saturday both the military and protestors agreed to form a joint civilian military body to pave the way for a civilian government.
But the two sides are at odds over numbers.
The military are pushing for a 10-member council including seven military representatives and three civilians, while the protestors want a 15-member council with seven military representatives and eight civilians.
Adding to the deepening discord, the military council says that six security personnel were killed and 16 were wounded in clashes with protesters across the country late Monday.
The Sudanese Professionals Association (SPA) said the army was trying to remove barricades and disperse the sit-in outside army headquarters, although witnesses said troops had not moved in.
The deputy head of the military council insisted it was "not against" the Khartoum sit-in while Lieutenant General Salah Abdelkhalik said that the army "will never use violence against protesters".