The United Nations called on both sides to pull forces from disputed territories and return to negotiations. South Sudan pulled its troops from Abyei last week and Sudan was called on to do the same.
Ban said Khartoum should pull out in accordance with international agreements. Both sides should "immediately" set up an administrative district in the area to normalize the situation, he said through his spokesman.
South Sudan gained independence under the terms of a 2005 agreement that ended one of the bloodiest civil wars in modern history. Unresolved issues like border demarcation and disputes over oil, however, threaten the deal.
Khartoum said it would pull out once an administrative body was agreed to by South Sudan, the independent Sudan Tribune reports. A security vacuum would develop in the region without arrangements for border areas, the Sudanese government said.