The referendum commission's website announced on Sunday that 98.7 percent of the votes had been counted.
The referendum was promised under a 2005 north-south peace deal which ended Africa's longest civil war. A vote for secession was widely expected because of persistent tension between the mainly Muslim north and southerners who mainly Christian or follow traditional religions.
"As of now, 100 percent of the North and (overseas) votes and 98.7 percent of the South votes have been processed," the commission's website (http://southernsudan2011.com/) said.
The provisional and incomplete results showed that 98.81 percent of voters wanted secession, it said, confirming earlier returns.
The votes need to be sent to the commission's headquarters in Khartoum for checking before the preliminary results are announced in a week. The south is likely to declare independence on July 9.
Exactly how the two will disentangle their economies, share oil wealth and demarcate the border remain to be decided.
The disputed central Abyei region remains the major sticking point as both sides claim the area, which saw deadly clashes between tribes during the week-long referendum this month.
Most analysts believe neither north nor south wants or can afford a return to all-out war. The south's budget is 98 percent derived from oil, most of which is produced in the south, but which is refined, transported and administered by the north.
Both sides have used proxy militias which could provoke wider clashes.
The civil war between north and south, fuelled by differences over oil, ideology, ethnicity and religion, claimed an estimated 2 million lives and destabilised much of east Africa.