President Omar al-Bashir - wanted on war crimes charges related to the 13-year conflict - has insisted voting go ahead on whether to unite Darfur's five states into a single region, or maintain the status quo.
A united Darfur with greater autonomy has long been a demand of ethnic minority insurgents battling the Sudanese government since 2003, but they have boycotted the referendum, saying it is unfair.
Analysts say nothing much is at stake and that the outcome will most likely favor the current five-state system, which they say gives Khartoum greater control over the breakaway region.
This referendum was supposed to take place after the Doha agreement of 2011, a peace agreement signed between the Sudanese government and Liberation and Justice Movement rebels.
"The picture the government is portraying, and the Information Minister, Ahmed Bilal, has come out and say that this is the most peaceful time since 2003 that Darfur is enjoying peace, that Sudan is fulfilling its commitments under the peace agreement that it signed with some of the opposition groups in 2011 and their commitment is there, and they're securing the referendum in that way," Ahmed Soliman, a political analyst from the London-based Chatham House, told RFI.
"But obviously, regarding the provisions of the Doha agreement, it remains to be seen that they've been fulfilled - cessation of all hostilities and a permanent cease-fire; protection of human rights and freedom for civil society groups; power sharing and administrative status of Darfur; and sharing of wealth. All of these things are still to be resolved, but you have this picture beeing painted that Darfur is coming together."
According to Eric Reeves, a Sudan researcher and analyst at Smith College, there is absolutely nothing at stake here, he said this was an entirely Khartoum concocted political event.
Furthermore, he said the international community's lack of action enabled Sudan to go through with this referendum.
"The regime believes, with good reasons and much evidence, that it has been embraced by the international community, sufficiently so that it needn't worry about sanctions or UN resolutions, and it is in violantion of some two dozens of UN resolutions," Reeves told RFI.
"The outreach by the UK is particularly distressing and send a particularly ill-timed and unfortunate signal to the regime but Serbia giving Omar al-Bashir its medal of honour, Poland reaching out, various European countries, including France, speaking about debt relief for a regime that has produced colossal 48 billion dollars in external debt... all this is music to Khartoum's ear."
There have been reports of heavy fighting taking place in the Jebel Marra region of Darfur since January, and according to experts, the government, by holding the referendum, wants to say to the rest of the world that nothing's going on, everything's fine. The proof? They're having the long awaited referendum.
Also, the humanitarian situation has gotten worse over the past few months.
"There's been reports of gender-based and sexual violence, mass rapes... In fact our researchers have been looking into crimes commited by the Rapid Support Forces, who are a new version of the Janjaweed militias," Akshaya Kumar, the deputy United Nations director at Human Rights Watch, told RFI.
"And on top of all that, you have a dire humanitarian crisis, millions who still live in camps, further displaced. And people who are now been displaced. So the situation is not much better, and it's simply not the time to try to move forward and pretend like people in Darfur still not experiencing abuses and crimes."
She says this has been the government's modus operandi. They have for years prevented international organisations, NGOs, journalists etc, to work in Darfur.
Analysts say that it's about time the international community stopped turning a blind eye to what's happening in Darfur.
"I think it's important to underline that the international community is rather ambiguous about that, especially now that the EU is obsessed with preventing more refugees to come. So it's actually alining with the regime that has been creating the refugees in order to prevent them to come, just keep them at home," Jerome Tubiana, a Sudan specialist with the Small Arms Survey, told RFI.
"Everyone is underlining the EU process of dealing with the refugees in this part of the world is called the Khartoum process and it's basically an agreement with the government of Sudan to get money and take care of the problem at home. It is just like if one would give money to Bashar al-Assad to deal with the Syrian refugees."
The referendum is the last step in a peace process negotiated in Doha. Rebels have long requested more regional powers to end what they see as Khartoum's interference in land ownership conflicts - but nothing guarantees that this is about to change.