Sudan's ruling generals and protest leaders reached an agreement on the disputed issue of a new governing body on Friday, in a breakthrough power sharing accord aimed at ending the country's months-long political crisis.

The landmark agreement came after two days of talks following the collapse of the previous round of negotiations in May over who should lead the new ruling body — a civilian or soldier.

Read: Timeline: Key events in Sudan’s unfinished revolution

"The two sides agreed on establishing a sovereign council with a rotating military and civilian (presidency) for a period of three years or little more," African Union mediator Mohamed El Hacen Lebatt told reporters.

Sudan has been rocked by a political crisis since the army ousted longtime ruler Omar al-Bashir in April on the back of widespread protests, with the generals who seized power resisting demonstrators' demands to hand it over to a civilian administration.

"We want to reassure all political forces and armed movements and all those who took part in the change ... that this agreement is all inclusive and does not exclude anyone," deputy chief of the ruling military council General Mohamed Hamdan Dagalo said in a statement.

Tension between the two sides had further soared after a brutal raid on a longstanding protest camp outside army headquarters in the capital Khartoum that killed dozens of demonstrators and wounded hundreds on June 3.

Read: Tens of thousands protest army rule in Sudan

Lebatt did not specify the exact make-up of the new ruling body, but prominent protest leader Ahmed al-Rabie told AFP that it would comprise of six civilians, including five from the protest movement, and five members of the military.

The latest round of talks had resumed on Wednesday after intense mediation by Ethiopian and African Union envoys, who had put forward a draft proposal to break the weeks-long deadlock.

'Independent investigation' into raid

The blueprint proposes a three-year transition period, with the president of the new ruling body to be held by the military for the first 18 months and a civilian for the second.

However, it was still unclear if both sides had signed off on the military holding the post first.

Lebatt, however, said the two sides had agreed to postpone the forming of a new transitional parliament.

Before talks collapsed in May the generals and protest leaders had agreed on forming a 300-member parliament, with two-third of lawmakers to be from the protest movement.

Lebatt said that both sides have now also “agreed to have a detailed, transparent, national, independent investigation into all the regrettable violent incidents that the country faced in recent weeks,” including the June 3 raid.

Read: Sudan denies more than 100 killed in protest crackdown

At least 136 people have been killed across the country since the raid, including more than 100 on June 3, according to doctors close to the umbrella protest movement, the Alliance for Freedom and Change.

The health ministry says 78 people have been killed nationwide over the same period.

That raid was carried out by men in military fatigues.

The ruling military council insists it did not order the violent dispersal of the sit-in.

For weeks the issue of forming the new ruling body has rocked Sudan, extending the political crisis triggered by the fall of Bashir.

Prior to the start of the latest round of talks on Wednesday, Ethiopian mediator Mahmoud Drir had said that the thorny issue of the new governing body was "the sole point of disagreement" between the two parties.

Students march for civilian rule

Protest leaders have exerted pressure on the generals since the June 3 raid on the mass sit-in.

On Sunday, protest leaders managed to mobilise tens of thousands of supporters in the first mass protest against the generals since the raid.

The mass rally had been seen as a test for the protest leaders' ability to mobilise crowds after the generals imposed a widespread internet blackout and deployed security forces in the capital's key squares and districts, its twin city Omdurman and other towns and villages.

On Thursday hundreds of students from several schools in three towns — Madani, Gadaref and Sinnar — staged spontaneous protests chanting "civilian rule, civilian rule," witnesses said.

Earlier on Thursday, a group of 235 fighters from a faction of a Darfur rebel group that is part of the protest movement were released as decided during the talks.