Egyptian Armed Forces Commander in Chief Abdel-Fattah al-Sissi announced on national television on Wednesday evening that the head of the country's Supreme Constitutional Court would act as president.
A national unity government pending early elections would be formed, he said.
One of the Islamist Egyptian president's top advisers earlier on Wednesday had condemned action by the country's army as a "military coup" after an ultimatum for Morsi to forge a deal with opponents expired.
"For the sake of Egypt, and for historical accuracy, let's call what is happening by its real name: military coup," Essam al-Haddad, who is Morsi's national security adviser, said in a statement on Facebook.
Troops and armored personnel carriers were reported to be moving near to the scenes of pro-Morsi protests, including a central one outside the Rabia al-Adawiya Mosque. The Reuters news agency said troops had also deployed outside a barracks where Morsi was said to be working and that the building was being surrounded with barbed wire.
Meanwhile, the state-run Al-Ahram newspaper reported that the military had placed several leaders of Morsi's Muslim Brotherhood under surveillance and imposed a travel ban on them. The news agency DPA reported sources at Cairo airport as saying that a travel ban on Morsi himself was related to the president's 2011 escape from prison during the uprising that toppled former President Hosni Mubarak.
Al-Ahram, which is understood to be under the control of the military, said forces had been deployed in Cairo "to prevent any dangerous acts of violence that might threaten Egyptian national security in the coming hours."
In a last minute statement before the deadline expired between 4 p.m. and 5 p.m. local time (1400 to 1500 GMT), Morsi himself criticized the military for "taking only one side."
He added that respecting his electoral legitimacy was the only way to prevent violence. In a statement posted on his Facebook page, Morsi called for national dialogue to end the political crisis.
Opposition spokesman Mohamed ElBaradei, along with Egypt's top Muslim cleric and a Coptic pope had met General Abdel Fattah al-Sisi for talks on measures that the military threatened to impose on Wednesday. Those discussions came to an end on Wednesday evening, with a statement to be released by the army on a new roadmap for transitional rule.
Threat of imposed solution
On Monday, the Egyptian army had given Morsi 48 hours to reach a compromise deal with the opposition - or face an imposed military solution.
The political wing of the Muslim Brotherhood reportedly refused an invitation to meet with the armed forces commander, and promised to stand firm against any pressure brought by the army for Morsi to step down. In a late night speech Tuesday, Morsi said that he would not resign and that doing so would threaten Egypt's constitutional legitimacy - stressing that he had been elected in "free clean elections."
The president was elected in a close runoff with 51.7 percent of the vote last June, becoming the country's first democratically elected president.
At least 16 people were killed and more than 200 wounded on Wednesday in overnight clashes. Unknown gunmen had opened fire on Morsi supporters who were rallying outside Cairo University.
rc/mkg (AFP, AP, dpa, Reuters)