The roundup which placed some Brotherhood members in the same prison holding Hosni Mubarak the autocratic leader toppled in the 2011 revolution came as a senior jurist was sworn in as the acting head of state.
In a ceremony broadcast live on state television the chief justice of the Supreme Constitutional Court Adli Mansour took the oath and praised the protesters whose mass demonstrations spurred the Egyptian military to depose Mr. Morsi on Wednesday suspend the Constitution and install an interim government. Mr. Mansour said the actions in Egypt had corrected the path of its glorious revolution.
Both Mr. Mansour and the National Salvation Front an alliance of liberal and leftist parties that had pushed for Mr. Morsi s ouster offered an olive branch to his Islamist supporters in the Muslim Brotherhood saying that the group was part of the spectrum of Egyptian society and should participate in an inclusive political process.
But the Muslim Brotherhood which had long been banned in Egypt until the 2011 Arab Spring revolution and quickly shot to power under Mr. Morsi appeared to rule out any reconciliation arguing that the military intervention was a coup that overthrew Egypt s legitimate leader.
We reject participation in any work with the usurper authorities Sheik Abdel Rahman al Barr an executive board member of the organization said in a statement on the group s Web site which also exhorted members to show self restraint and stay peaceful.
At the same time Egypt s public prosecutor on Thursday ordered the arrest of the supreme guide of the Muslim Brotherhood Mohamed Badie and his influential deputy Khairat el Shater on charges of incitement to kill demonstrators. Egyptian media said Mr. Badie was taken into custody later Thursday.
The flagship state newspaper Al Ahram said the two Islamist leaders were suspected of playing a role in the deaths of eight protesters six by gunshots while a mob was attacking and burning the Muslim Brotherhood s headquarters in Cairo earlier this week.
The arrests appeared to be part of a broadening crackdown on Mr. Morsi and his political allies that included the arrests of dozens of Muslim Brotherhood members. Ahram Online the English language Web site of the state newspaper said those taken into custody included Saad el Katatni leader of the Muslim Brotherhood s Freedom and Justice Party and Rashad Bayoumi the deputy head of the Islamist movement.
Shortly before Mr. Mansour was sworn in the skies over the capital Cairo filled with military jets in a series of flybys news reports said. The state run MENA news agency reported that the flights were meant to celebrate the triumph of popular will.
Tahrir Square where tens of thousands of opponents of the government had gathered each night since Sunday to demand Mr. Morsi s removal erupted in fireworks and jubilation on Wednesday night at news of the ouster but by Thursday the city was reported to be calm.
At a square near the presidential palace where Mr. Morsi s Islamist supporters had gathered men broke into tears and vowed to stay until he was reinstated or they were forcibly removed. The dogs have done it and made a coup against us they chanted on Wednesday. Dying for the sake of God is more sublime than anything a speaker declared.
Military vehicles and soldiers in riot gear had surrounded the pro Morsi rally in the hours before the takeover and tensions escalated through the night. Within hours at least seven people had died and more than 300 were injured in clashes in 17 provinces between Mr. Morsi s supporters and either civilian opponents or security forces.
Just before he was taken into custody Mr. Morsi rejected the generals actions as a complete military coup. By the end of Wednesday night Mr. Morsi under house arrest was blocked from all communications one of his advisers said.
For Mr. Morsi it was a bitter and ignominious end to a tumultuous year of bruising political battles that ultimately alienated millions of Egyptians. Having won a narrow victory his critics say he broke his promises of an inclusive government and repeatedly demonized his opposition as traitors. With the economy crumbling and with shortages of electricity and fuel anger at the government mounted.
David D. Kirkpatrick reported from Cairo and Alan Cowell from London. Reporting was contributed by Kareem Fahim Mayy El Sheikh and Ben Hubbard from Cairo Mark Landler from Washington and Rick Gladstone and Mona El Naggar from New York.
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