Despite calls from demonstrators to halt the negotiations, opposition leaders from the FFC and TMC ruling generals resumed talks on Thursday evening, according to journalists on the ground.
The authorities have also declared a state of emergency in the area and imposed night-time curfew since the shootings.
Ahead of Thursday's talks, FFC leaders said the coalition has resolved major sticking points in the talks, a move that brings them closer to finalising a power-sharing deal.
Thursday's rallies denounced those killings, which took place when crowds of students demonstrated against growing commodity shortages.
Many carried Sudanese flags and photographs of some of those people killed in the months-long protest campaign. In the days that follow, opposition-linked medics say more than 100 people were killed in the assault.
"The force which was guarding the Sudanese French Bank fired the live rounds that led to the regrettable losses in the state of North Kordofan", Lieutenant General Jamal Aldin Omar Ibrahim, head of the Transitional Military Council's security committee, was quoted as saying by SUNA. Sudan's military assumed power, but June 3 the military opened fire and murdered more than 100 protesters outside the military's headquarters, intensifying worry that Sudan would become a military dictatorship. The Sudanese Professionals Association said Thursday that the rallies are demanding justice for the killing of at least six people, including four students, earlier this week during student protests in a central province.
A doctor at Al-Obeid hospital who received the casualties told AFP that four of those killed were students.
The Al-Obeid rally was to protest weeks of shortages of bread and fuel.
This happened after months of nationwide protests that broke out in December after his government chose to triple the price of bread.
That body would then establish a transitional civilian administration for a period of just over three years, after which elections would be held.
Monday's killings in Al-Obeid triggered global outrage, and Burhan condemned the incident as an "unacceptable crime" that called for swift accountability.