Rebels in Sudan's Darfur region will become victims of improved relations between Khartoum and Juba as South Sudan reduces its support for the insurgency, Darfur's top official said on Tuesday.

In an interview, Eltigani Seisi also said security forces used excessive force last week against "innocent civilians" protesting high prices in Darfur. At least eight people were shot dead.

Seisi heads the Darfur Regional Authority set up to implement a peace deal last year between the Khartoum regime and an alliance of rebel splinter factions.

He said that although security has improved "very much" since the Doha Document for Peace in Darfur, over the past two or three months rebels outside the peace process crossed into Darfur from South Sudan to launch attacks.

"Everybody knew that they were in southern Sudan. Everybody knew that they are supported by southern Sudan," he said, in a reference to independent South Sudan which separated in July last year.

"I think the (armed) movements must have realised that they have been used by southern Sudan to strengthen their position in Addis Ababa," he said at his Khartoum office.

Sudan and South Sudan fought along their undemarcated frontier in March and April, sparking fears of wider war and leading to a UN Security Council resolution which ordered a ceasefire and the settlement of critical unresolved issues.

The South says it does not support the rebels. Darfur's main rebel group, the Justice and Equality Movement, has denied any presence in South Sudan but suspected JEM members were seen alongside Juba's troops during the border fighting.

After weeks of fragile talks in the Ethiopian capital, Sudan and South Sudan reached a breakthrough agreement last Saturday over fees due by Juba for shipping its oil through the north's pipeline for export.

"The way I see it now, the two countries are moving to harmonise their relations and the rebel movements have become victim to that," said Seisi, a former governor of Darfur who also worked as a United Nations adviser.

The Doha peace pact was the fruit of talks sponsored by the African Union, UN and Arab League.

JEM and factions of the Sudan Liberation Army, another key group, refused to sign.

JEM said the pact did not resolve key issues including power and wealth sharing, human rights violations, and the almost two million displaced by the war.

The peace document does, however, call for a truth and reconciliation committee, a special court to handle cases of gross human rights violations, support for reconstruction and development, compensation for refugees, and affirmative action for Darfuris in government and military service.

JEM and SLA later joined ethnic rebels from South Kordofan and Blue Nile states in a "revolutionary front" to overthrow the Khartoum government by force.

JEM and SLA, drawn from black African tribes, rose against the Arab-dominated Khartoum government in 2003 and were confronted by state-backed Janjaweed militia in a conflict that shocked the world.

Unrest continues but is much less than at its peak nearly a decade ago.

UN Secretary General Ban Ki-moon reported last month that many provisions of the Doha deal are behind schedule, including the transfer of an initial $200 million from Khartoum for a reconstruction and development fund.

"It's absolutely necessary for us to get the $200 million. Otherwise nobody will be tempted to contribute to the reconstruction and development of Darfur," Seisi said.

Villages were razed in the conflict which has left almost two million people still displaced in camps.

Sudan's President Omar al-Bashir is wanted by the International Criminal Court for war crimes allegedly committed in Darfur.

A new spurt of unrest in the past week saw security forces shoot dead protesters in the South Darfur city of Nyala, and troops deployed in the North Darfur town of Kutum where eight people died during looting and other violence.

The Nyala deaths were the first officially confirmed since Arab Spring-style protests sparked by inflation began in the Sudanese capital in June.

"The force was excessive," Seisi said. "We saw demonstrations in other parts of the country (but) nobody has lost his life."

In Kutum, district chief Abdelrahman Mohammed Eissa was shot dead during a carjacking attempt, Seisi said.

Members of Eissa's tribe retaliated with looting and attacks on a camp for the displaced, he said, adding four camp residents, two police and two soldiers were killed but the town is now under army control.

The UN's World Food Programme compound was among the premises ransacked.

"There is an ethnic and tribal polarisation in Darfur," Seisi said. "It has started with the war."