Stating that sovereignty over the Nuba mountains, the southern Blue Nile and Abyai were not up for discussion, Umar al-Bashir's comments on Wednesday potentially raise a major obstacle to a peace deal.
The three contested areas on the border between north and south are among a number of issues standing in the way of a deal between the government and the rebel Sudan People's Liberation Army (SPLA), who have been at war for two decades.
Although the two sides signed an accord in the Kenyan town of Naivasha on how to share wealth, there is as yet no agreement on power sharing or territory.
Delegates at talks mediated by the regional Intergovernmental Authority on Development (IGAD) had hoped to begin discussing land disputes this week.
But speaking about sovereignty to the official Sudan News Agency, Sudan's president said there was "no mandate to resolve this issue in the current talks in Naivasha".
"One issue [only] in the peace talks on southern Sudan remains - that is participation in power."
Bashir said the government had in the past agreed to a dialogue on the territorial dispute only "out of respect for the other side" and on condition that it did not form part of the IGAD peace initiative.
"One issue [only] in the peace talks on southern Sudan remains - that is participation in power"
president of Sudan
He said the government would oppose any attempt to redraw the border between northern and southern Sudan.
Reduced opportunity for peace
His remarks implied that a formal agreement was possible even without a deal on the border.
Several senior members of the SPLA come from the disputed areas, which are currently part of the north.
There was no immediate reaction from negotiators on either side, who have been working to lessen differences between the government and southern regions seeking more autonomy and control over local resources.
Sudan's southern civil war has killed about two million people and displaced four million more.
In July 2002 the sides reached a deal granting the south a referendum on secession after a six-year interim period that begins after combatants agree a final peace accord.