Sudan's military ruler offered to resume talks with opposition groups without conditions on Wednesday, in an apparent olive branch two days after security forces mounted a deadly raid on a protest camp in central Khartoum.

Lt.-Gen. Abdel Fattah al-Burhan's offer marked a step-back from the army's decision to cancel all deals with the opposition after the raid — and came as international criticism of the violence mounted.

Sudanese opposition medics said Wednesday evening that the death toll from the country's recent violence has risen to 108, a sharp increase from the beginning of the day.

The opposition said the toll went up after 40 bodies were recovered from the Nile river in Khartoum. It is the worst outbreak of violence since the army ousted president Omar al-Bashir in April following months of mass protests against his rule.

State news agency SUNA early on Thursday put the number much lower, at 46, citing a health ministry official.

Sudan's ruling Transitional Military Council said it had launched an investigation into the recent violence.

"The council has initiated an independent investigation ... an urgent and transparent investigation with fast results," said the council's deputy chairman, Gen. Mohamed Hamdan Dagalo, commonly known as Hemedti. "Any person who crossed boundaries has to be punished."

Sudan's opposition and protest groups, who have kept up their demonstrations since Bashir's overthrow, have pressed the army to hand over power to a civilian government.

In this frame grab from video provided by Sudan TV, Lieutenant General Abdel-Fattah Burhan, head of the Sudanese Transitional Military Council, TMC, makes a statement the day after a pro-democracy sit-in outside the army command base in the capital Khartoum was violently overrun by the ruling army. (Sudan TV/The Associated Press)

They quickly rejected the ruling military council's invitation to resume talks, because "it is not a source of trust."

"[The council] is imposing fear on citizens in the streets," Madani Abbas Madani, a leader of the Declaration of Freedom and Change Forces (DFCF), told Reuters.

Military leaders and the opposition groups have been haggling for weeks over who should lead the transition to democracy.

The opposition's mood is likely to be improved by reports that a Sudanese rebel leader who returned from exile after the overthrow of Bashir was arrested on Wednesday.

Yasir Arman, the deputy head of the Sudan People's Liberation Movement-North (SPLM-N) group, came back last month and joined other opposition groups meeting the military leaders who ousted Bashir, according to local media reports.

Arman was detained by security services at his house in Khartoum, a spokesperson for the SPLM-N said, without giving any details on the reasons.

Yasser Arman, who had recently returned to Sudan from exile was reportedly detained on Wednesday according to the group he represents, the Sudan People's Liberation Movement-North. (Ashraf Shazly/AFP/Getty Images)

No one was immediately available to comment from the security services.

Arman had been sentenced to death in absentia for his part in a rebellion against Bashir's government that started in the Sudanese state of Blue Nile in 2011.

Several streets in other parts of the capital were blocked by demonstrators on Wednesday. Gunfire rang out in the distance, but there were no immediate reports on new clashes.

Less activity than earlier in week

Most shops were shuttered on what would usually have been a bustling Muslim Eid al-Fitr holiday, with minor protests erupting outside mosques after Eid prayers.

"We in the military council, extend our hands to negotiations without shackles except the interests of the homeland," Burhan, the head of Sudan's ruling military council, said on state TV.

He praised the uprising's achievements and reiterated that he was ready to hand over to an elected government.

The military has denied it was trying to clear the sit-in protest outside the defence ministry on Monday. Its spokesperson said forces moved in to deal with disruptive groups nearby and the violence spread from there.

Sudanese top opposition leader and former premier Sadiq al-Mahdi adresses worhippers during the Eid al-Fitr prayer marking the end of the Muslim holy fasting in Omdurman, just across the Nile from the capital Khartoum. (AFP/Getty Images)

Sudan has been rocked by unrest since December, when anger over rising bread prices and cash shortages broke into sustained protests that culminated in the armed forces removing Bashir after three decades in office.

In the build-up to the raid, talks had ground to a halt between the Transitional Military Council and DFCF amid deep differences over who would lead a transition to democracy.

Omar al-Degair, a prominent DFCF leader, said on Tuesday the two sides had been close to reaching a final deal on a plan that would have involved a 50-50 military-civilian split on a council to prepare the transition, and a rotating presidency.

The alliance has already rejected the military's offer, made since the raid, of elections in coming months.

U.S. National Security Adviser John Bolton said in a Twitter post that Monday's violence by Sudan's security forces was "abhorrent" and demanded that the military council facilitate moves toward a civilian-led government.

Saudi Arabia, which has close ties to Sudan's military council, said on Wednesday it was watching developments with great concern.

"The Kingdom hopes that all parties in Sudan will choose wisdom and constructive dialogue to preserve security and stability in Sudan, protect the people of Sudan from all harm, while maintaining Sudan's interests and unity," a statement on the official Saudi Press Agency said on Wednesday.

Sudan's opposition Democratic Alliance of Lawyers on Tuesday urged "some Arab countries" not to interfere in Sudanese affairs and to drop their support for the military council — comments apparently aimed at Saudi Arabia, the United Arab Emirates and Egypt.