As southern Sudanese prepare to vote for independence tomorrow, the jubilation at the prospective breakup of Sudan that is so widespread in the south is not shared by everyone in the north.

Particularly concerned are people in the two "contested areas" – South Kordofan and Blue Nile – who fought alongside the southerners in the civil war but have been left in the north by Sudan's comprehensive peace agreement (CPA).

With predominantly African populations of Nuba and Ingessana, who practise Christianity and traditional religions in addition to Islam, the people of the two areas are now being referred to as janubeen jadeed – the new southerners. This reflects their potential future status as marginalised Africans on the southern periphery of an integrated Arab-Islamist state. Precisely the same situation that led to the southerners calling for independence.

To complicate matters, virtually all of north Sudan's current oil production is in South Kordofan. If Southerners vote to secede, Khartoum stands to lose the 80% of its oil supplies currently produced in the south, and is unlikely to countenance losing the rest.

Under the CPA, the two areas are supposed to have "popular consultation" on their future status, but this process – like the referendum for Abyei district – is completely off-track and people are extremely nervous about their future should the south vote to secede and President Omar al-Bashir carry out his threat to amend the constitution to consolidate north Sudan as an Arab-Islamic state with no concessions for racial or religious minorities.

Bashir recently declared: "If south Sudan secedes, we will change the constitution, and at that time there will be no time to speak of diversity of culture and ethnicity … sharia and Islam will be the main source for the constitution, Islam the official religion and Arabic the official language."

This statement – coupled with his defiant stance on Islamic law after international condemnation of a YouTube video of a woman being flogged by laughing policemen – has caused massive unease among north Sudan's minorities. Bashir said those calling for an investigation into the ill-treatment misunderstood Islam, because "sharia law has always stipulated that one must whip, cut, or kill".

Kamal Kambal, of Nuba Mountains Solidarity Abroad, says: "This is the reason why the southerners want to break away, and of course it is also going to be a disaster for those of us who are going to be forced to live with people with this mindset." Pointing out that the Nuba had been fighting alongside the south "to prevent the imposition of sharia law and Arabic culture", Kambal adds: "For us, this statement is a declaration of war."

He says this is an especially sensitive issue for the Nuba because, during a state-sponsored jihad against the Sudan People's Liberation Army (SPLA) in the Nuba mountains in the 1990s, the government issued a fatwa proclaiming Muslim rebels to be apostates who had renounced Islam, giving free rein to the pro-government Popular Defence Force militias, who were largely recruited from among Misseriya Arab pastoralists. He points out that the state elections stipulated by the CPA have been postponed in South Kordofan, where the current governor is Ahmed Mohamed Haroun, who has been indicted by the international criminal court for war crimes in Darfur.

He also points out that Bashir has threatened to expel the UN from north Sudan immediately after the referendum, and that now "his plans to rewrite the constitution are going to undermine all the provisions of the CPA in northern Sudan".

"Bashir clearly doesn't recognise the rights of anyone other than Arabs and Muslims," Kambal says. "He allowed cultural and religious freedom for minorities while he wanted to keep the southerners on board, but what rights will Christians and minority people like the Nuba have after the south breaks away?"

He believes that Britain and the CPA's other international guarantors are "currently only concerned about the south and the referendum, and have forgotten about the CPA's protocol on the two contested areas, which stipulates 'popular consultation' on the future status of South Kordofan and Blue Nile".

Ahmed Hussein Adam, spokesman for Darfur's Justice and Equality Movement, says: "This has revealed the true face of President Bashir and gives a clear indication of the type of state we're going to be left with after the separation of the south.

"Bashir is trying to impose one religion, one culture and one ethnicity over Sudan's diverse population. This will unfortunately lead to more violence as there is no way that everybody will accept this. It is a declaration of war against Darfur, the Nuba, the people of Blue Nile and the entire marginalised majority of Sudan."

The UN recently expressed concern about the "uncertain fate" of southerners living in northern Sudan and northern Sudanese in the south. It has made preparations for a worst-case scenario, with contingency plans which anticipate that almost 3 million people could be displaced if fighting breaks out due to disputes over the referendum.