After speculation that Omar Hassan al-Bashir, who had been serving a prison sentence, had been freed, the army said that he was being held in a military hospital but provided no evidence.
Washington had hoped to work with other countries during the pause to help permanently end the fighting. Instead, the warring generals violated it just hours after it began.
The clashes have killed more than 400 people and injured thousands more. Those displaced are streaming into nations such as Chad, Egypt and South Sudan, adding to a refugee crisis in the region.