Partial results posted on the Southern Sudan Referendum Commission website showed that with 3,197,038 ballots counted, 98.6% had voted to break away in the January 9-15 referendum.
In the state of Jonglei, a massive 99.93 per cent of votes were in favour of secession, the figures showed. Only 77 voters supported Sudan's unity, while 105 people cast blank or invalid ballots.
The first results from the state of Western Equatoria also revealed that, based on the votes counted so far, 99.5 per cent chose secession.
The results published Friday are incomplete as several hundred thousand votes remain to be counted to account for the 96 per cent turnout announced by officials earlier this week.
"Some few counties still remain to submit their results, so the figures are not complete yet, and we are continuing to work hard to finalise the results," said Aleu Garang Aleu, spokesman for the Southern Sudan Referendum Bureau, which is running the vote in the south.
Some south Sudanese also voted in the north and abroad.
"We are still expecting that the results for the south will be released on 31 January, and, allowing time for any appeals, the final result will be announced in Khartoum on 14 February," he said.
The independence vote is part of a 2005 peace deal between the Khartoum government and southern rebels that ended a 22-year civil war between the mainly Muslim, Arab north and the mainly Christian, African south.