Secession will involve Nuba people being ruled by Khartoum with scant hope that the south will support its calls for autonomy

As southern Sudan prepares for independence on Saturday, residents of the Nuba mountains near the new border are pushing for a breakaway state rather than affiliation with the north or the south.

The region lies in the Arabised north of Sudan, although its people have long been sympathetic to the south. But conflict in the area in recent weeks has cast a shadow over independence and bodes ill for the stability of Sudan after partition.

"There is no way for me to be part of the north anymore," said 35-year-old Yohanes Mudier. "I haven't fought for so many years just to fall under the same government again."

Like many of his fellow Nuba, Mudier joined southern Sudan's rebel movement at the start of the 1983-2005 Sudanese war to support what he thought would be a struggle towards freedom. He spent 14 years in the Sudan People's Liberation Army (SPLA) without seeing his family. When he came back to the Nuba mountains in 2006, after peace deals had been signed, many of his relatives were dead.

Mudier says there is no reason for him to celebrate independence. "I am part of the SPLA, but I feel I have been left behind. We will never get anything out of Khartoum through a political process. There is no point in talking to them any more."

His remarks reflect the views of a growing number of Nuba who feel betrayed by all the players involved in the peace agreement: the Sudanese government, the international community, and the Sudan People's Liberation Movement (SPLM), the political wing of the SPLA. Most Nuba are still affiliated with the northern wing of the movement, but many would prefer independence to joining the south.

In the past weeks, the SPLM-dominated government in south Sudan has stressed that it will not engage in another war against Khartoum. Still bearing the scars of 20 years of a devastating conflict, the leadership of the south will focus on development rather than putting its new sovereignty in jeopardy by throwing its military weight behind the Nuba people.

There are those who still have faith in the SPLM, insisting that after Saturday's independence, troops and weapons will start flowing from Juba, the capital of south Sudan, to the Nuba mountains.

But others, such as Montasir Nasir Waren Kalo, are more sceptical. In 2005, he was part of a Nuba youth delegation that lobbied the SPLM not to sign the peace agreement. "We have been the wheel of freedom for the whole African people of Sudan, but we never enjoyed the fruits of our struggle. We were always sacrificed for the benefit of others, and the [peace deal] is no exception to that," he said.

The recent misfortunes of Nuba started in 2005 when John Garang, the long-time leader of the SPLA/M, died in a helicopter crash a few days after the war ended. His Mandela-style vision of a united "new Sudan", where Arabs and Africans would coexist under a new political leadership, was then substituted by the new SPLM leaders with a more achievable goal: the independence of the south.

But according to the 1956 Sudanese borders, on which the peace agreement is based, the Nuba mountains will fall under the control of the north. "When I read the conditions of the [peace deal], I thought the southern leadership had sold us off," said a local social worker, who asked not to be named for fear of retaliation.

"When the SPLM/A was marred by internal division in the 90s, Nuba were the ones who supported Garang. Without us, the movement would have died and the south would have never been independent."

Instead of the referendum on independence given to southerners, the Nuba mountains were granted only ill-defined "popular consultation" to express their opinion on the peace deal. Six years later, no date has been set for the consultations. Many here believe the Khartoum government will never allow them to take place.

Nuba are divided between those who want complete independence, and those who still support the SPLM/A as the best hope of freedom; but they are united in their determination to control their own destiny. "A wrong peace is worse than a war," said a Nubian SPLM MP, who asked for anonymity. "We would rather take our weapons again to achieve a just one, than settle for the current situation."

His opinion is shared by Mudier: "If the south does not help us, we will have to fight the northern regime to the last man," he said. "Maybe only our grandchildren will see that day."

• This article was amended on 4 July 2011. Some references to the people of the Nuba mountains described them as "Nubians". While it may be the case that this term is sometimes used in speech in the Nuba mountains, it has been changed throughout the article above for the avoidance of confusion with the people of Nubia – a different people inhabiting a different region.