Sudanese leaders and rebel commanders agreed Monday on a historic peace deal, a crucial step towards ending 17 years of conflict in which hundreds of thousands of people were killed.

Leaders of the Sudan Revolutionary Front (SRF), an umbrella organization of rebel groups from the western region of Darfur and the southern states of South Kordofan and Blue Nile, raised their fists in celebration after inking the agreement.

Fighting in Darfur alone left around 300,000 people dead after rebels took up arms there in 2003, according to the United Nations, with former government leaders accused of carrying out genocide and of crimes against humanity.

Conflict in South Kordofan and Blue Nile erupted in 2011, in the wake of South Sudan's independence, resuming two decades of war.

"I congratulate all in Sudan on reaching a historic comprehensive peace that addressed the roots of the problem and ended the war, God willing," said Gibril Ibrahim, commander of one of rebel groups, the Justice and Equality Movement (JEM).

Sudanese paramilitary commander Mohamed Hamdan Daglo who commanded fighters in the war, signed the deal on behalf of Khartoum. 

The agreement covers key issues around security, land ownership, transitional justice, power sharing, and the return of people who fled their homes because of fighting.

It also provides for the dismantling of rebel forces and the integration of their fighters into the national army.

Rebel members of the Sudan Liberation Movement (SLM) and  the Sudan People's Liberation Movement-North (SPLM-N) had provisionally initialed the agreement with the government late on Saturday.

However, an SLM faction led by Abdelwahid Nour and a wing of the SPLM-N headed by Abdelaziz al-Hilu refused to take part.

"We have started the real transformation of Sudan from dictatorship to democracy," Faisal Mohammed Salih, Sudan's information minister said at the ceremony in Juba, the capital of neighboring South Sudan.

But while celebrating the deal, he said there was also still a long way to go.