At least five protesters and a member of Sudan's army were reportedly killed on Monday as violence erupted outside the military headquarters in the capital, Khartoum.

The violence took place after opposition groups and the military council struck a deal for the country's political transition, following the ouster of President Omar al-Bashir last month.

Since then, protesters have been camping outside the military headquarters to support a civilian-led political transition.

'Unidentified elements' or 'militias'?

It remains unclear which group attacked the protesters. The military council said the attackers belonged to armed groups who were unhappy with the political deal's progress.

Protesters, on the other hand, said military elements linked to al-Bashir's former regime were to blame.

Read more: Sudanese military: A pawn of the Saudis?

"Some unidentified elements who wanted to spoil negotiations between the two sides tried to enter the sit-in... and gunshots were fired that led to the killing of a major from the military police," the military council said.

The doctors' committee linked to Sudan's protest movement said a young man had been shot in his chest by "the ousted regime militias who attempted to disperse the Sudanese peoples' sit-in."

Transition deal reached

Prior to the clashes, Taha Osman, a spokesman for the protest movement, told the Agence France-Presse news agency that a deal had been reached on "the structure of the authorities and their powers."

"The authorities are as follows: the sovereign council, the cabinet and the legislative body," he said.

Read more: Sudan protests: Female force in action

Osman added that another meeting was scheduled for Tuesday "to discuss the period of transition and the composition of the authorities."

The military council also confirmed that the deal had been reached. "We agreed on forming the transitional authority on all three levels," council spokesman Lieutenant General Shamseddine Kabbashi told reporters.

"Tomorrow we will continue to discuss the percentage of participation... and the transitional period," he said.

Disagreement exists on that issue, with the generals insisting the transitional period last two years. Protesters want it to last four years.

Earlier Monday, Sudan's prosecuting authority charged al-Bashir for his role in protesters' deaths during the uprising.

Prosecutors will also investigate a case of money laundering against the ousted president after large amounts of cash in various currencies were found in his home, state agency Suna reported.

jcg/cmk (AFP, Reuters, dpa)

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