People queued for hours in the burning sun outside polling stations in the southern capital Juba, and many were turned away as the first day of voting ended in the week-long ballot.

"This is the moment the people of southern Sudan have been waiting for," southern president Salva Kiir said after casting his ballot, urging people to be patient as they waited to vote.

The referendum was promised in a 2005 peace deal ending a civil war which has raged on and off since 1955, fueled by oil and ethnicity, between the mostly Muslim north and the south, where most people follow Christianity and traditional beliefs.

The war left two million dead and displaced four million people and Southerners view the poll as a new beginning after decades of strife and perceived repression by north Sudan.

Polls closed at 1400 GMT on Sunday but from Monday, voting hours would be extended until 1500 GMT, the electoral commission said. Most centers have no power so voting ends at sundown.