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. The ruling party in South Sudan, which is set to become independent in July, says the vote was rigged.
Analysts fear the dispute could spark yet another conflict in Sudan. A civil war is still raging in Darfur, while some 1.5 million people died during decades of conflict between north and south. The International Criminal Court accuses 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. Haroun defeated Abdelaziz al-Hilu, a senior official of South Sudan's Sudan People's Liberation Movement (SPLM), according to the official results. Could Nuba mountains be the next Sudan conflict? "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 region 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. (BBC)