Muslim Brotherhood leader Mohamed Badie has been detained, according to Egyptian security sources.
The prosecutor’s office ordered the arrests of Badie and up to 300 other members of the Brotherhood following the overthrow of Mursi, who was backed by the group.
According to military decree, Mursi’s successor Adly Mansour will serve as interim president until elections are held.
Supporters of the ousted leader say they are appalled by what has happened over the last couple of days. They accuse the army of breaking the law by intervening to depose a democratically-elected president.
One Mursi supporter protesting in Cairo, said: “They’ve been lying to the people and seconds after the declaration they stopped all the Islamic TV channels. This is not freedom. They’re arresting people without court orders. We’re back to Mubarak.”
Muslim Brotherhood leaders have pledged to hold peaceful protests in response to Mursi’s removal.