The detentions came as a collection of Islamist groups led by the Muslim Brotherhood called on Egyptians to hold nationwide protests on Friday after Morsi's ouster.
The National Coalition in Support of Legitimacy "calls on the Egyptian people to take to the streets and mobilize peacefully" after Friday prayers "to say no to military detentions, no to the military coup," Reuters reported.
On Thursday, the coalition held a news conference at a mosque in Cairo, where supporters of the ousted president have been holding a sit-in.
In a statement posted on the Muslim Brotherhood's English-language website later on Thursday, the group said it remained committed "to peaceful demonstrations and restraint and that it will not be drawn into violence."
The statement, attributed to Muslim Brotherhood spokesman Ahmed Aref, also described the Egyptian government as a "brutal police state which has resumed repressive practices."
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For Brotherhood supporters gathered at Thursday's sit-in, the detentions and political changes are evidence of a betrayal and a coup, CBC's Nahlah Ayed reported from Cairo, adding that many Morsi supporters have vowed to stay put until the deposed leader is restored.
Other Egyptians argue that the rapid change in the Arab world's most populous nation is a move in the right direction.
Nourhan El Shaer told Ayed that what happened in Egypt was "not a military coup at all."
"It's a revolution, it's a great revolution," she said Thursday.
Morsi is a member of the Muslim Brotherhood, and Egypt's military has been cracking down on the group since the coup, seizing its TV station and replacing Morsi with a senior judge who will lead an interim caretaker government.
Muslim Brotherhood supreme leader Mohammed Badie was arrested Wednesday night in a Mediterranean coastal city west of Cairo near the Libyan border, Egyptian officials said. The officials spoke Thursday on condition of anonymity because they were not authorized to speak to the press.
Badie, who was flown to Cairo in a military helicopter, is on a wanted list of more than 200 Brotherhood officials, including his deputy Khairat el-Shater, and leaders of other Islamist groups.
The country's official news agency said Badie and el-Shater were being sought for questioning about their role in the killing of eight protesters in clashes outside the group's Cairo headquarters. The two men were believed by the opposition to be the true power in the Morsi administration.
Egyptian judicial authorities have also opened an investigation into accusations that Morsi and 15 other Islamists had insulted the judiciary, investigating Judge Tharwat Hammad said Thursday.
"Clearly, it's a pretty strong clampdown on the Muslim Brotherhood and certainly one that is likely to eventually draw some kind of reaction," Ayed said earlier Thursday.
The Brotherhood has also announced it would boycott the new military-sponsored political process and called on its supporters to restrain themselves and not use violence.
The powerful and well-organized Brotherhood has dominated the political scene since the 2011 removal of president Hosni Mubarak.
New interim leader
Earlier Thursday, Supreme Constitutional Court Chief Justice Adly Mansour took a leadership oath in a small room surrounded by just a handful people in the Cairo court beside the Nile, replacing Egypt's first freely elected leader after only a year in office.
The judge and now interim leader, speaking on live TV, praised the protesters who began holding massive demonstrations four days ago in a bid to oust Morsi, saying they had united Egyptians.
"The most glorious thing about June 30 is that it brought together everyone without discrimination or division," he said. "I offer my greetings to the revolutionary people of Egypt."
Ayed said that the new president saluted protesters, youth, and the military. The military was notably absent from the ceremony.
"He said that the Egyptian people have proved to the world that they do not bend. He declared the era of dictators in Egypt over."
Mansour's short speech was met with long applause and cheering in the chamber where the oath took place, she said.
In Tahrir Square — the epicentre of both the country's 2011 revolution and this week's protests — Egyptians reacted to the swearing in with honking and fireworks. Military jets with contrails in the colours of the Egyptian flag flew overhead.
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Ayed said Mansour is not well known to the outside world, but is known in Egypt. A lawyer, he became head of the Constitutional Court a few months ago.
According to military decree, Mansour will serve as Egypt's interim leader until a new president is elected. A date for that vote has yet to be set.
Morsi is under house arrest at an undisclosed location and is not allowed to leave the country. Initial reports Wednesday suggested Morsi was detained at the presidential guard facility where he had been staying, but by Thursday Morsi's precise location was unclear.
He was ousted after the military's 48-hour ultimatum to share power or step down expired Wednesday afternoon local time. Morsi denounced the military's actions as a "full coup."
CBC's Derek Stoffel, also in Cairo, reported that Egypt's Health Ministry says 10 people were killed and 481 injured in clashes after the coup, meaning around 50 people have been killed since the new round of protests began.
Many were still celebrating the changes Thursday, but others in Egypt have concerns about the change and the military's role, Stoffel reported.
"This will make it like a police country, army country — they control everything, as before," said lawyer Adel Emam.
Ayed said there is a sense of urgency in the country and that new elections could happen quickly, within a few months.
'Will of the people'
The clock started ticking for Morsi when millions took to the streets on Sunday to demand he resign a year after he was elected. They accused his Muslim Brotherhood of hijacking the 2011 democratic revolution, entrenching its power and failing to revive the economy.
That gave armed forces chief Gen. Abdel-Fattah el-Sissi, who already had his own reservations about the state of the nation under Morsi, a justification to invoke the "will of the people" and demand the president share power or step aside.
Sissi's road map wipes clear a slate of messy democratic reforms enacted since Mubarak fell.
An interim government will be formed, along with a panel for national reconciliation. The constitution will be reviewed, presidential and parliamentary elections arranged.
There was no timetable. Liberal chief negotiator Mohamed ElBaradei, a former UN nuclear agency chief, said the plan would "continue the revolution" of 2011. Many hope they can have more electoral success than last year, when the Brotherhood's organization dominated the elections.
Even with an interim leader in place, Egypt remains on an uncertain course after Morsi's ouster, and the possibility of further confrontation looms. Beyond the fears about violence, some protesters are concerned whether an army-installed administration can lead to real democracy.
UN Secretary General Ban Ki-moon spoke to Egypt's Foreign Minister Mohammed Kamal Amr Thursday and expressed "deep concern" about the military intervention.
A statement from the secretary general's spokesperson said Ban "stressed the need for a quick return to civilian rule in Egypt based on a clear roadmap for election" and cited the need for a peaceful, inclusive dialogue.
Foreign Affairs Minister John Baird’s press secretary issued a statement on Wednesday, saying "Canada urges all parties in Egypt to remain calm, avoid violence and engage in meaningful dialogue.
"Canada firmly believes that implementing a transparent democratic system that respects the voices of its citizens, and that encourages and respects the contributions of civil society and all other segments of the population, including religious minorities, is the best way to restore calm and give all Egyptians a stake in the future stability and prosperity of Egypt."
- Why the U.S. doesn't call Egypt military's ouster of Morsi a coup
U.S. President Barack Obama was cautious in his response, acknowledging the "legitimate grievances of the Egyptian people" while also observing that Morsi, an Islamist, won his office in a legitimate election.
He notably stopped short of labelling Morsi's ouster a coup, leaving himself some wiggle room to navigate a U.S. law that says its government must suspend foreign aid to any country whose elected leader is ousted in a coup d'etat.
David Jacobson, the U.S. ambassador to Canada, told CBC News that the most important thing is that the U.S. supports inclusive, democratic governments.
"We hope that there will be no violence, we hope that there will not be unnecessary arrests, and we hope that an inclusive, democratic government will be re-installed as soon as possible," Jacobson said.Suggest a correction