The arrests appeared to counter the army's promises to prevent attacks on Morsi's supporters and new President Adly Mansour's intent to lead a government "inclusive of all political factions."
The Muslim Brotherhood's spokesman Gehad El-Haddad said Morsi had been put under house arrest Wednesday night. and "hundreds of names" of Brotherhood leadership had been added to an "arrest list."
The wanted include Mohammed Badie and Khairat el-Shater, the leader of the Muslim Brotherhood and his deputy, who were often considered the power behind Morsi's presidency, allegedly for the deaths of eight protesters killed in clashes outside the Brotherhood's Cairo headquarters.
El-Haddad also confirmed the arrests of Saad el-Katatni and Rashad Al-Bayoumi, the chief and deputy of the Brotherhood's Freedom and Justice Party.
Meanwhile, Morsi was defiant. He issued a statement, taped and delivered to the news agency Al Jazeera.
"The world is looking at us today," he said. "We by ourselves can bypass the obstacles. We, the sons of Egypt, the sons of this country -- this is the will of the people and cannot be canceled."
Al Jazeera's Cario headquarters, along with the Muslim Brotherhood's television station, Egypt25, and other news channels accused of being pro-Morsi were shut down. Some staff members were detained and later released.
"I don't believe closing down any newspaper or any channel is a useful measure... but we are going through a very critical time here, the situation is dangerous," said a spokesman for the National Salvation Front. "I hope this is an exceptional measure that will last only for a few days, but when you have a critical time of change like this and you have some other people who are trying to incite supporters to go and fight I don't think it is useful to have these channels working at these critical hours."
A "deeply concerned" President Obama, in a carefully measured response to the tumult, warned the newly installed government against making arrests of the ousted leadership and urged President Mansour to quickly hold legitimate elections to restore a democratically elected government.
"The voices of all those who have protested peacefully must be heard -- including those who welcomed today’s developments, and those who have supported President Morsi," he said. "In the interim, I urge all sides to avoid violence and come together to ensure the lasting restoration of Egypt’s democracy."