Morsi was detained along with senior aides after issuing a defiant call for supporters to protect his elected "legitimacy", in a recorded speech hours after the military announced he had been ousted Wednesday.

"We had to confront it at some point, this threatening rhetoric," the military official said.

"He succeeded in creating enmity between Egyptians," the official said.

At least 50 people were killed in clashes in the days leading to massive protests on June 30 calling for his departure.

That prompted the army to issue the president a 48-hour ultimatum to find an agreement with the protesters.

Morsi has been summoned for questioning by a court over his escape, along with other inmates, from prison during the revolt that overthrew his predecessor Hosni Mubarak in 2011.

The military official suggested he may now be charged by prosecutors in the case.

A senior member of Morsi's Muslim Brotherhood has earlier told Morsi and senior aides had been detained in a military facility.

"Morsi and the entire presidential team are under house arrest in the Presidential Republican Guards Club," Gehad El-Haddad, the son of a top Morsi aide, told.

Haddad's father, Essam El-Haddad, widely seen as Morsi's right-hand man, was among those held, he added.

The military official did not specify where Morsi is being held. Haddad said the ousted president was separated from his aides and detained at the defence ministry.

Morsi's top aides have switched off their phones. Other presidential aides who were separated from Morsi earlier in the day say they have lost communication with their leader.