Ninety protesters were killed in protest-related violence after demonstrations erupted in December over a government decision to triple the price of bread, a doctors' committee linked to the protest movement said last month. Local doctors said some were in serious condition.
The military council claimed "lurking groups" who were unhappy with the announcement of an agreement with the protesters lay behind the attack.
The Alliance for Freedom and Change - the protest movement umbrella group that has been negotiating with the military council - said the shootings were an attempt to "disturb the breakthrough" and blamed militias still loyal to Bashir's regime.
The apparent progress was offset by rising tension in the capital Khartoum, where paramilitary forces patrolled the streets into the evening, using tear gas and gunfire to disrupt protests blocking roads.
The next round of talks are set to discuss two sticking points: the military-civilian balance of power in transitional bodies, and the length of the transition before elections.
Opposition forces say supporters of former president Omar al-Bashir are responsible for the attack.
Three soldiers and several protesters and civilians were also wounded when "unidentified elements" fired shots at the Khartoum sit-in Monday night, the ruling military council said.
The major and a protester were killed at a sit-in outside the army headquarters in Khartoum where thousands of protesters remain camped for weeks, demanding that the army generals who took power after ousting Bashir step down.
The crucial talks between Sudan's army rulers and protest leaders over handing power to a civilian administration follow a deadlock in negotiations.
"There are plenty of violent specialists with a pedigree in terror who will seek to ruin any meaningful democratization of Sudan", said Harry Verhoeven, author of 'Water, Civilization and Power in Sudan.' "The surprise is, in any sense, that this did not come earlier". General Mohamed Hamdan Dagalo, head of the RSF and deputy head of the TMC, told a military meeting on Monday that the armed forces and RSF were working to protect "security and stability" in Sudan.
Also on Monday, Sudan's public prosecution said it had charged Bashir and others with incitement and involvement in the killing of protesters.
"Will it work? Well let's see whether or not Omar al-Bashir ever faces trial", she said, noting that although the prosecutor has already accused Bashir of money laundering and financing terrorism, "there has been no sign that any kind of judicial proceeding is imminent".
Bashir was imprisoned in the capital, Khartoum, days after the military removed him from power.