His defence minister, armed forces chief General Abdel Fattah al-Sisi, announced Morsi’s overthrow on state television, even as police began rounding up key Morsi aides and leaders of the Muslim Brotherhood.
Warrants have been issued for the arrest of a total of 300 Brotherhood officials, state media reported.
Thousands of protesters camped out on the streets of Cairo for days celebrated wildly at the news of Morsi’s downfall, letting off fireworks and sounding car horns.
But at least seven of Morsi’s supporters were killed in clashes with security forces in Alexandria and the eastern city of Marsa Matrouh, security officials said.
The official MENA news agency also reported three people killed in the southern province of Minya when pro-Morsi supporters attacked the Islamist’s opponents.
Already in the week leading up to Morsi’s downfall, at least 50 people have died in clashes between the Islamist’s supporters and opponents.
Morsi and his senior aides were “under house arrest” in a military facility, a senior Muslim Brotherhood member told AFP.
The ousted president was later taken to the defence ministry, Gehad El-Haddad added. His father, senior Morsi aide Essam El-Haddad, is one of those detained.
Police also began arresting leaders of Morsi’s Muslim Brotherhood movement, an interior ministry general told AFP. Saad al-Katatni, head of Morsi’s Freedom and Justice Party, was already in custody, he added.
Morsi issued a defiant call for his supporters to defend his elected “legitimacy” in a prerecorded speech posted online after Sisi’s statement.
Thousands of his supporters remained camped out in northern Cairo, but Egyptian television stations stopped broadcasting live feeds of the pro-Morsi rally after the military announced his overthrow.
US President Barak Obama said he was “deeply concerned” over Morsi’s ouster and urged the army to refrain to “arbitrary arrests” of Morsi and his supporters.
In May, Washington approved $1.3 billion in military aid to Egypt. That was now under review, said Obama, as he called for a swift return to democratic rule.
In his speech, Sisi laid out details of the roadmap for a political transition.