Most of the people who voted against independence were southerners who cast their ballots in the north. The commission feels that concern over the voters own safety led the people in the north to vote that way.
Southern Sudan received this right to vote for freedom from a 2005 peace deal that ended a long civil war.
From Reuters, writers Jason Benham and Jeremy Clarke detail the latest results from the historic vote.
The website for the Southern Sudan Referendum Commission (http://southernsudan2011.com/) showed a 98.6 percent vote for secession, with more than 80 percent of the votes from the south counted, and 100 percent counted in other areas.http://www.trust.org/alertnet/news/update-1-almost-99-percent-choose-south-sudan-split
The commission earlier confirmed the turnout had passed the 60 percent mark needed to make the result binding.
Officials from the oil-producing south have so far given a measured response to the early results and warned voters not to stage early celebrations to avoid antagonising the north.
The calm, controlled mood in the southern capital Juba has been in sharp contrast to the jubilant scenes that greeted the start of voting, when campaign posters described independence as a liberation from war and northern oppression.
"This is the outcome we expected ... the results won't change much," the commission's deputy chairman Chan Reek Madut, a southerner, told Reuters.
The only area to show a majority for unity was a small pocket of voters in the northern Sudanese state of South Darfur. According to the figures, 63.2 percent of voters wanted to keep the country together and only 36.8 percent went for secession.
"It is not surprising because of the way they conducted their registration. Some people passed as southerners who were actually northerners from Darfur," said Madut.