"If the demands of the people are not met within this period, it will be incumbent upon us to announce a road map for the future and oversee measures to implement it."
But in a statement issued later, the presidency insisted it would continue on its own path towards national reconciliation.
The army declaration had not been cleared by the presidency and could cause confusion, it said.
The presidency also denounced any declaration that would "deepen division" and "threaten the social peace".
Morsi was consulting "with all national forces to secure the path of democratic change and the protection of the popular will", it added.
"The civil democratic Egyptian state is one of the most important achievements of the January 25 revolution," said the presidency, referring to the 2011 uprising that toppled dictator Hosni Mubarak.
"Egypt will absolutely not permit any step backward whatever the circumstances," it added.
The army announcement had appeared to stun the Brotherhood and supporters of Morsi, who until the marches were launched were confident that only a minority of people, mostly loyal to the former regime of Mubarak, supported opposition calls for him to quit. There was no sign that Morsi had been informed in advance of the army's move, even though Sisi is a member of Morsi's Cabinet and Morsi is technically head of the Supreme Council of the Armed Forces.
It is not clear if it means the army will force Morsi to step down - or whether he would do so if it was demanded of him. But many of the protesters on the streets believed the army would at least order fresh elections - a key demand. Tamarod, the grassroots campaign behind the huge protests, hailed the statement by the armed forces which it said had "sided with the people". It "will mean early presidential elections", Tamarod's spokesman Mahmud Badr told reporters.
In tumultuous scenes, drivers in Cairo honked their horns and waved national flags out of their windows. Several army helicopters flew over Tahrir Square proudly trailing the national flag. Tens of thousands of jubilant protesters also poured into the streets of Alexandria and other large cities after the statement was broadcast. In Tahrir, protesters voiced their support for al-Sisi, chanting: "Come down Sisi, Morsi is not my president."
But 16 people died in protests on Sunday and Monday, including eight protesters in clashes between supporters and opponents of the President outside the Cairo headquarters of the Muslim Brotherhood.
The police had refused to defend the Brotherhood property, and in the clashes that ensued gunshots were exchanged. Witnesses said that although there was firing from both sides, the Brotherhood supporters in the building were protected by sandbags.
An Egyptian reporter, Salah al-Din Hassan, 37, was killed by a homemade bomb while covering anti-Morsi protests in Port Said. The Dutch Embassy in Cairo said that a 22-year-old Dutch woman, who according to Egyptian news reports was a television reporter, was repatriated after being raped on Saturday in Tahrir.
The violence demonstrated the Brotherhood's inability to command the authority of the police, a power base of the Mubarak regime. It not only refused to protect Brotherhood buildings, but several of its officers took part in the protests, even addressing the crowds in Tahrir.
- AFP