Southern Sudan's President Salva Kiir has said during a visit to Malakal that militia will not be tolerated in the town after clashes there last week.
Mr Kiir is also Sudan's national vice-president
At least 150 people died in fierce fighting between former rebels from the south and Sudan's national army.
The BBC's Jonah Fisher in Malakal says it was the most serious breach of the 2005 deal to end two decades of war.
The port river town is calm but tense with troops lining the streets and many residents still in shock, he says.
United Nations peacekeepers in the area have been helping both sides bury their dead.
Over the weekend, the UN warned that some corpses had contaminated a portion of the Nile River and water purification tablets were being distributed.
Under the peace deal, the former rebel Sudan People's Liberation Army (SPLA) joined a power-sharing government of which SPLA leader Mr Kiir is also vice-president.
Mr Kiir delivered his firm message to a rally on the outskirts of the town where violence broke out last week when a militia leader, Maj Gen Gabriel Tang, refused to hand over control to the SPLA.
There has been a long dispute between the two groups over control of an area near Malakal, located on the banks of the Nile near Sudan's oilfields.
During 20 years of civil war, Khartoum armed numerous ethnic militias in the area to enable it to begin extracting oil.
After Gen Tang took shelter in a Sudanese army base, a full-scale battle ensued.
Tank mortars and shells rained down on Malakal as the two partners in Sudan's government of national unity traded blows.
For Khartoum, Malakal's problems and that of the surrounding area are southern in nature and an issue that Mr Kiir must deal with, our correspondent says.
The two years of uneasy partnership between the Christian SPLA and the mainly Muslim Arab north has failed to tackle the numerous armed groups near the country's oilfields.
Malakal is a busy port town on the banks of the Nile
But our correspondent says the former rebels see last week's violence as something much more sinister.
Khartoum is continuing to arm and back the militia, a spokesman said, with the aim of destabilising the south and wrecking the peace agreement.
There are 10,000 UN peacekeepers deployed in southern Sudan at a cost of $1bn a year.
Under the terms of the peace deal, some army units are supposed to merge and these clashes were between troops who are officially part of the same force.
Unlike the continuing conflict in the western region of Darfur, Sudan's north-south ceasefire has largely held but few militiamen have handed in their weapons.