North and South have already endured decades of warfare, and the South is expected to vote for a split.
In the latest hurdle, North Sudanese leaders declared it would be impossible to carry out a referendum in the oil-rich district of Abyei, which has to decide whether to go with the North or South Sudan.
"We have reached agreement that it is not possible to hold the vote in Abyei on 9 January," Al-Dirdiri Mohammed Ahmed from the ruling National Congress Party told reporters Thursday.
Earlier in the week, talks in Ethiopia on who should be eligible to take part in the Abyei vote collapsed, and Sudanese President Omar al-Bashir warned that a "more dangerous" conflict could erupt if the disputes are not resolved before the referendum.
Speaking to the U.N. Security Council on Thursday, a top U.S. diplomat confirmed that South Sudan's president, Salva Kiir, had expressed concerns that war could break out.
"President Kiir also warned that he fears the North may be preparing for war and may be moving troops southward," said Susan Rice, U.S. envoy to the U.N., who recently returned from a trip to Sudan.
The U.N., which already has peacekeepers in Sudan, has decided to move some of its troops near the north-south border within the next few weeks.
The Sudanese government in Khartoum certainly isn't happy about the prospect of a split because it could lose large oilfields in the South and in Abyei.
The North could lose 80 percent of its oil reserves, 50 percent of the oil revenues, a third of its land and 30 percent of its population, said Scott Gration, President Barack Obama's special envoy to Sudan.
"So they're still seeking to make unity attractive," Gration said last month.
But the South has made it clear that the split is inevitable.
The referendum is a critical component of the 2005 Comprehensive Peace Agreement that ended a two-decade-long war between the South, which is Christian, and the predominantly Arab and Muslim government of the North.
An estimated 2 million lives were lost in the civil war. The Bush administration was a key player in brokering a peace deal, and the Obama administration has dispatched senior officials to Sudan to help organize the vote.
Sudan, which is Africa's largest nation, is juggling two crises at the same time. In the western region of Darfur, Arab militias allegedly sponsored by the Khartoum government have been accused of mass murder and rape of black residents. While the situation in Darfur has made international headlines, South Sudan has received far less attention.
Movie star George Clooney has sought to change that by paying a recent visit to South Sudan.
"What struck me the most is their resolve," Clooney said on "Larry King Live." "These are people who have been captured and sold and they have been tortured and they have been raped and murdered and they believe that they have the right for independence now.
"Every single on of them said, they are willing to fight and die for that freedom," he added. The actor said that since the U.S. already invests billions of dollars in the country, "the question will be whether we're going to spend that money mopping up a massacre."
Voices from the ground indicate the situation goes beyond the North-South divide. Opoka Christopher, who teaches journalism in Juba, the capital of South Sudan, pointed out that the majority of the South Sudan wants to secede -- but many people are also sick of the corruption and ineptitude of their own government.
Christopher also said there is a great deal of ignorance among the people of South Sudan, many of whom don't realize the implications of their decision.
"The South will vote for separation, few knowing and understanding the importance of their vote," he said. He said only the elite class realizes that governing the desperately poor region would be impossible, but they are not speaking out.
Speaking at the U.N. meeting on Sudan in September, Obama warned Sudanese leaders that failure to carry out a fair referendum would lead to grave consequences from Washington. "More pressure and deeper isolation," he said.
At the same meeting, the African Union also expressed its support for the referendum. However, many African nations are not keen on the split because of the "instability" and "dangerous precedent" it will set on the continent.
"They are dreading this," a top U.N. diplomat said, speaking on condition of anonymity.