Sudanese protestors on Thursday "totally" rejected the military offer to resume talks after more than 100 demonstrators were killed in the raids.
"We in the military council extend our hand for negotiations without shackles except for the interests of the homeland," Aljazeera quoted General Abdel Fattah al-Burhan as saying.
But a Sudanese alliance of protesters and opposition groups rejected the offer, saying the military could not be trusted.
"Today the council invited us to dialogue and at the same time it is imposing fear on citizens in the streets," Mad Abbas Mad, a leader of the Freedom and Change alliance.
The talks between the military and the demonstrators have collapsed after the armed forces fired upon the peaceful protestors on Monday.
Earlier the Central Committee of Sudanese Doctors said that the 46 people have been killed in Monday raids.
However, at least 40 bodies were further recovered from the Nile rivers.
This comes as a setback to ongoing talks to achieve peace in the country. This might also delay the process of establishing a civilian rule.
Last month, after the series of talks, Sudan's military has reached a power-sharing agreement with the opposition alliance for a three-year transition period before a civilian government is elected.
The army generals had initially insisted on a two-year transition period, while the protest leaders wanted four.
Thousands of protesters have been holding a sit-in outside the army headquarters in the capital, Khartoum, for weeks, demanding the stepping down of Sudan's military leaders who seized power in April by overthrowing longtime ruler Omar al-Bashir.
Some of them also expressed caution over the prospects for an agreement that would satisfy their demands.
( With inputs from ANI )