Polling centres closed at 6pm (1500 GMT) at the end of the three-day referendum to decide whether to unite Darfur’s five states into a single, autonomous region, with a handful of voters coming to cast their votes late.
“The centres are closed now and the operation went well,” said Omar Ali Jomaa, head of the referendum commission.
The commission did yet not have turnout figures as many centres were in remote areas where communication is difficult, he said.
Insurgents who since 2003 have battled the government of President Omar al-Bashir boycotted the referendum.
A single, autonomous region has long been a demand of the rebels but they said ongoing unrest in Darfur meant the vote would be unfair.
Bashir, whose ruling National Congress Party supported the five-state system, insisted the ballot take place as it was stipulated in a 2011 peace agreement signed with some rebel groups.
Washington and Paris had criticised the election, saying conditions in the region meant the result might not be credible.
Heavy clashes between troops and the Sudan Liberation Army led by Abdulwahid Nur in the Marra mountain range at the heart of Darfur have forced at least 100,000 people to flee their homes since mid-January, the UN says.
Ethnic minority rebels mounted an insurgency against the Arab-dominated government in Khartoum 13 years ago, complaining the region was being marginalised.
There are more than 2.5mn people displaced by the conflict living in the region and 300,000 people have been killed in the conflict, according to the UN.
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