Lt. -Gen. Shams al-Deen al-Kabashi, a spokesperson for the military council, said Monday's meeting, the first in over a week, was held "in a more optimistic atmosphere". They don't want to be caught unawares when the forces come for them.
Sudan's protesters say they will not cede ground to the military rulers and have vowed to continue their demonstrations outside the army headquarters until all their demands are met.
Sudan's ruling military council said Tuesday that a brother of ousted president Omar al-Bashir who it previously announced had been detained was actually not in custody.
The charges form part of an investigation into the death of a medic during a protest in Khartoum's eastern district of Burri.
Talks resumed on Monday, and both sides said they had produced agreement on the duties and authorities of sovereign, executive and legislative bodies.
According to a doctors' committee linked to the protest movement, 90 protesters were killed in protest-related violence after demonstrations began in December over a government decision to triple the price of bread. But Sudan's ruling military council has said it would not extradite him to the ICC at The Hague. The official death toll is 65.
A Reuters witness said police, backed by the paramilitary Rapid Support Forces, dismantled barriers that were erected by protesters at the entrance to the bridge, causing traffic jams.
Prior to the meeting, dozens of protesters blocked Nile Street, a major avenue in the city, for the second consecutive day, an AFP correspondent reported.
Since 6 April, thousands of protesters have been holding a continuous sit-in in front of the headquarters of the General Command of the Sudanese Armed Forces in Khartoum to pressure the Transitional Military Council to hand over power to civilians.
On Saturday, the Alliance for Freedom and Change - an umbrella for the protest movement - said the generals had invited it for a new round of talks after several days of deadlock.
The protests have so far given them the only leverage they have against the military council and they are not about to let it go.
Late last month, the alliance - which brings together protest organisers, opposition parties and rebel groups - handed the generals its proposals for a civilian-led transitional government. They have singled out the alliance's silence on the constitutional position of Islamic sharia law, which was the guiding principle of all legislation under Bashir's rule.
Demonstrators converged on the military complex last month seeking the army's help in ousting him.
A military council assumed power of the country on 11 April, but demonstrators are insisting that it hands over to a civilian administration.
The killings took place after nightfall on Monday, when protests in Sudan usually swell during the Muslim holy month of Ramadan that is marked by dawn to dusk fasting.