The Sudanese Professionals Association (SPA) did not say who was attempting to break up the crowd, but witnesses said several army vehicles had surrounded the area.
"There is an attempt to disperse the sit-in from the army headquarters area, they are trying to remove the barricades," the SPA said in a statement to AFP.
"We call on our people to come immediately to the sit-in area to protect our revolution."
Witnesses said troops were seen removing the barricades that demonstrators had put up as a security measure.
"Protesters are chanting 'army is our army'," an onlooker told AFP from the site of the sit-in.
Witnesses said the army displayed a banner on one of the walls of their building facing the protesters.
"Our brothers and sisters, don't come close. You have been our guests under our protection. But now the emergency law governs all of us," the banner said.
On Monday Sudan's military council said it was restructuring the military command council and had appointed Colonel General Hashem Abdel Muttalib Ahmed Babakr as army chief of staff.
Colonel General Mohamed Othman al-Hussein was appointed as deputy chief of staff, the council's statement added.
Before his ouster last week, veteran president Omar al-Bashir imposed a state of emergency under which rallies were banned.
The SPA described the attempt to disperse the crowds as "an indication that the military council will not fulfil its committment given to the people", in a separate statement on its Facebook page.
Protest organisers have given a list of demands to the country's new ruling military council that came to power after Bashir was removed from office.
Their key demands include handing power to a transitional civilian government and bringing leaders of Bashir's regime to justice, including the deposed president.
(FRANCE 24 with AFP and REUTERS)