He has been declared the winner of the governorship poll in the oil-rich South Kordofan state, which borders potential flashpoints Darfur and South Sudan.
South Sudan is set to become independent in July, while civil war is still raging in Darfur.
Analysts fear the dispute could spark yet another conflict in Sudan.
The International Criminal Court accuses Mr Haroun of mobilising Arab militias to commit genocide against black African residents of Darfur when he was the minister there in 2003-4. He has denied any wrong-doing.
President Omar al-Bashir is also wanted on similar charges.
'Dangerous times'Mr Haroun, from the president's National Congress Party, defeated senior SPLM official Abdelaziz al-Hilu, according to the official results.
"We will not accept these results because the vote was rigged," said Yasir Arman, head of the SPLM in the north.The SPLM fought the north for two decades before a 2005 peace deal, which paved the way for independence for the largely Christian and animist South Sudan from the mainly Muslim, Arabic-speaking north.
But many residents of the Nuba Mountains region of South Kordofan also fought for the SPLM and it is feared they could take up arms once more.
"These people were fighting for 20 years and their aspirations are not fulfilled," Hafiz Mohamed of the Justice Africa think-tank told the BBC's Network Africa programme.
"The way things are going, it's leading to a deadlock, which will end up with people carrying arms to release their frustration," he said.
"If it starts, no-one can stop it - it will affect the south, it will affect the north. With the war in Darfur, we are heading for dangerous times."
President Bashir has promised to accept South Sudan's independence but tensions have been rising recently over the disputed area of Abyei, which also borders South Kordofan.
Show regionsThe great divide across Sudan is visible even from space, as this Nasa satellite image shows. The northern states are a blanket of desert, broken only by the fertile Nile corridor. Southern Sudan is covered by green swathes of grassland, swamps and tropical forest.
Sudan's arid northern regions are home mainly to Arabic-speaking Muslims. But in Southern Sudan there is no dominant culture. The Dinkas and the Nuers are the largest of more than 200 ethnic groups, each with its own traditional beliefs and languages.
The health inequalities in Sudan are illustrated by infant mortality rates. In Southern Sudan, one in 10 children die before their first birthday. Whereas in the more developed northern states, such as Gezira and White Nile, half of those children would be expected to survive.
The gulf in water resources between north and south is stark. In Khartoum, River Nile, and Gezira states, two-thirds of people have access to piped drinking water and pit latrines. In the south, boreholes and unprotected wells are the main drinking sources. More than 80% of southerners have no toilet facilities whatsoever.
Throughout Sudan, access to primary school education is strongly linked to household earnings. In the poorest parts of the south, less than 1% of children finish primary school. Whereas in the wealthier north, up to 50% of children complete primary level education.
Conflict and poverty are the main causes of food insecurity in Sudan. The residents of war-affected Darfur and Southern Sudan are still greatly dependent on food aid. Far more than in northern states, which tend to be wealthier, more urbanised and less reliant on agriculture.
Sudan exports billions of dollars of oil per year. Southern states produce more than 80% of it, but receive only 50% of the revenue, exacerbating tensions with the north. The oil-rich border region of Abyei is to hold a separate vote on whether to join the north or the south.
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