Sudan's Second Vice President Moses Machar said here ahead of the meeting that Khartoum would put to an end to militia activities in regions that it controls, notably Eastern and Western Upper Nile states in central Sudan.
"If the problem is from the forces that are allied to the government, the Sudan govenment will have to take steps to stop it," Machar told reporters.
"If those militias have gone out of their way to break the ceasefire, it is time to show what the government of Sudan shall be doing," he said.
Machar's pledge came on the eve of the reconciliation conference in the Kenyan capital where Khartoum and the Sudan People's Liberation Movement/Army (SPLM/A) inked the deal to end nearly 21 years of civil war -- then Africa's longest-running conflict -- on January 9.
The former rebel army, its political wing and rivals as well as representatives from the Khartoum and pro-government militias are expected to attend.
About 30 militia groups, unaffected by the peace deal, continue to launch attacks in the Upper Nile states, hitting villages here, collecting illegal taxes and abducting locals, residents and aid workers told AFP this month.
The three-day conference aims to help southern Sudan's fractious factions take advantage of billions of dollars in post-war reconstruction aid pledged by donors and form a semi-autonomous government before August.
Despite the peace deal and the promised aid, tensions remain high between the government, its proxy militias in the south and the SPLM/A. Many militias have refused to deal with SPLM/A leader John Garang who they accuse of being dictatorial.
"We came with an open heart, our priority is peace," Machar said when asked about the prospects for the lingering resentment being overcome in Nairobi.
"You cannot deny the fact that when a people have been involved in a bitter struggle for the last 20 something years, it is not easy when the war stops that you easily come together and put things right," he said.
"We want to solve the problems," said Machar, who heads Khartoum's delegation.
SPLM/A officials have said they hope the meeting will be able to bridge differences between all sides in the south on the nitty-gritty of the peace deal and devise ways of dividing among themselves oil revenue that will be shared with the north under a complex formula in the agreement.
Sudan watchers say the conference offers an opportunity to completely pacify the region, the theatre of more than two decades of war between the largely Christian and animist south against the Arabised and Muslim north.
"The conference offers an opportunity to southern political and armed groups to define a common ground of the implementation of a peace deal," said David Mozersky, an Sudan analyst with International Crisis Group.
The conflict claimed at least 1.5 million lives and forced at least four million others to flee their homes.