The civil war forced more than four million people from their homes, creating the world's largest displaced population.
Most southerners who live in the slums have been relocated against their will. Their homes have been demolished and the land sold to investors.
They are often moved to desert areas far from their workplaces, with no transport links, running water, electricity or adequate healthcare. Many are desperate to return home to their birthplace.
More than 800,000 have already returned to the south from the many parts of Sudan where they had fled to escape fighting between the Sudan People's Liberation Movement (SPLM) and Khartoum.
The government hopes to help at least 150,000 in Khartoum this coming year to return home. But conditions for those making the journey south along the Nile are terrible, with mine-ridden roads and unsafe boats.
Militia attacks and illegal taxation on roads are further hazards. For many, the lack of facilities, food or clean water in the south meant that they went straight back to the north of the country.
Manyebi said facilities would be provided along the way and at destination points. Registration in the slums around Khartoum for those wishing to return will begin on November 19.
Similar programmes in other states of Sudan that house southerners who fled the fighting would begin at a later date, Manyebi said.
"Don't all come to Khartoum ... we will get to you," he told a news conference.
The central government will spend about $30m to complement the autonomous southern government's spending of $24m in the first year of the project, which could take years to complete.