The United Nations Refugee agency says around 55,000 displaced people have left northern Sudan and returned to the south in the last few weeks.
The UNHCR says this is putting a tremendous strain on an already fragile situation.
A referendum on southern independence is scheduled for 9 January. It was promised in a 2005 agreement that ended decades of civil war.
An estimated 2 million people were killed and 4 million fled during that period.
Contingency plans have been drawn up by the UNHCR in case another war breaks out.
The scenarios include up to 100,000 southern Sudanese being displaced to Uganda, 100,000 to Kenya, 80,000 to Ethiopia and 50,000 to Egypt.