Rebels in Darfur took up arms against the government in February 2003, accusing it of neglecting the barren area and arming militia to burn, loot and kill local farmers.
During the two-year violence, thousands of people have been killed and more than one million displaced.
Khalifa, also head of the Sudanese government delegation to peace talks with the Darfur rebels in Abuja, Nigeria, said the " negative signals" sent by the United Nations Security Council through its resolutions on Sudan emboldened the Darfur rebels to reject negotiations.
He added, however, that the international community's stance to Sudan showed at the donors conference in Oslo last week "sent positive signals", which called on the rebels to resume talks with the government unconditionally.
The UN Security Council adopted Resolution 1593 last month, which decides to refer war crime suspects in Darfur to the International Criminal Court in The Hague.
Sudan rejected the resolution, saying it lacks the base of objective justice and violates its sovereignty.