JUBA: 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 organisation 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 in the vast western region.

In 2003, according to the United Nations, with former government leaders accused of carrying out genocide and crimes against humanity.

Conflict in South Kordofan and Blue Nile erupted in 2011, in the wake of South Sudan's independence, resuming a war that had raged from 1983-2005.

"This is a truly historic day," Prime Minister Abdalla Hamdok said as he called on holdout rebel groups to join the deal he said would build "peace and stability" in Sudan.

"We are waiting for them," Hamdok said.

Gibril Ibrahim, commander of one of the rebel groups, the Justice and Equality Movement (JEM), paid tribute to all those killed or affected by the long years of violence.

"I congratulate all in Sudan on reaching a historic, comprehensive peace that addressed the roots of the problem and ended the war, God willing," Ibrahim said.

Sudanese paramilitary commander Mohamed Hamdan Daglo - best known by his nickname "Hemeti", and who commanded fighters in the war - signed the deal on behalf of Khartoum.

"This deal represents... a new dawn," he said.

Daglo and the leaders of the rebel movements grouped together and shook hands at the ceremony in Juba, the capital of neighbouring South Sudan which seceded from the north in 2011.

Then the former enemies briefly danced together.

South Sudanese President Salva Kiir - a former comrade to some of the rebels during Sudan's earlier civil war - hosted and mediated the talks.