The vote is scheduled for January.
It would allow the autonomous southern region -- which holds a majority of the nation's oil -- to secede from the north.
Fears that the process would cause more instability in the war-torn nation have sparked concerns among the international community.
"The worst case scenario is war. Nobody wants war, but both sides are preparing for war," said John Ashworth, a southern Sudan analyst. "There are still major stumbling blocks. We have just over a hundred days to the referendum, and virtually nothing is in place."
Analysts say that a failure in Sudan would have broader implications, including sparking instability in the region.
International aid agencies are urging world leaders to act as the referendum nears.
"Failure to act risks a new eruption of violence and threatens the future of Africa's largest country, with just over 100 days until the referendum to decide whether the south should remain part of Sudan," five international aid agencies said in a letter to world leaders.
Oxfam, The International Rescue Committee, Tearfund, World Vision and Christian Aid warned that the next three months will be crucial for Sudan. The aid agencies work in the nation.
"This meeting will show whether they have the commitment to make the financial and political investment needed to help Sudan have a peaceful future," said Kirsten Hagon, head of the Oxfam office in New York. "Today's decisions will affect the lives of millions of Sudanese people."
Meanwhile, Amnesty International called on Sudanese authorities Friday to halt what it described as the intimidation of journalists. The group said journalists are regularly detained for carrying out their work, while others have been tortured or tried on politically motivated charges.
"No credible poll can be conducted in an environment where freedom of speech is being so openly violated," said Rania Rajji, Amnesty International's Sudan researcher.
"The governments of north and south Sudan must ensure the vote is held in an atmosphere where all Sudanese can freely express their views and halt any further restrictions to freedom of expression."
Currently, Omar al-Bashir is the president of Sudan, while Salva Kiir serves as the president of the southern region and the nation's vice president.
The referendum was part of a 2005 peace agreement that ended two decades of violence between the north and the south. The conflict led to the deaths of 2 million people, many from starvation.
At stake in the referendum are Sudan's massive oil reserves, found mostly in the south, but still controlled by the government in the north.
The United Nations' General Assembly has addressed various issues, including Thursday meetings on the Mideast peace talks and the conflict between Islamist rebels and government forces in Somalia.
Before the Sudan discussion Friday, Obama will also hold separate meetings with President Ilham Aliyev of Azerbaijan and President Juan Manuel Santos Calderon of Colombia.
He will also attend a working lunch with ASEAN leaders and meet his Krygyzstan counterpart, Roza Otunbayeva, before departing for the White House.CNN's David McKenzie contributed to this report.