Reeling from what it called a military coup against democracy, the group said it would not work with the new political system.
The sweep against the Brotherhood leadership included the group's top leader, a figure venerated among its followers, General Guide Mohammed Badie. He was arrested late Wednesday from a villa where he had been staying at a Mediterranean coastal city and flown by helicopter to Cairo, security officials said.
The move against the Brotherhood raises deep questions over how Islamists will fit into Egypt's new political system after the military on Wednesday swept out Morsi, the country's first freely elected president. The military is installing a new civilian leadership to pave the way to new elections, saying it will stay out of politics.
The army says it did so in the name of millions of Egyptians who had taken to streets demanding he be removed. In the eyes of protesters, Morsi and the Brotherhood from which he hails had warped the democratic process. Many of them say the group has proven its anti-democratic nature and argue that its leaders committed prosecutable crimes.
But the Brotherhood remains a powerful force, with a highly organized membership nationwide.
The top opposition political grouping, the National Salvation Front, issued a statement Thursday saying, "We totally reject excluding any party, particularly political Islamic groups."
The Brotherhood announced it wanted nothing to do with the new political system.
"We declare our complete rejection of the military coup staged against the elected president and the will of the nation," the Brotherhood said in a statement that the group's senior cleric Abdel-Rahman el-Barr read to Morsi's supporters staging a days-long sit-in in Cairo.
"We refuse to participate in any activities with the usurping authorities," it said.
There are fears of a violent backlash from Islamists against the army move, particularly from hard-liners, some of whom belong to former armed militant groups. Clashes between Islamists and police erupted in multiple places around the country after the army's announcement of Morsi's removal Wednesday night, leaving at least nine dead.
Morsi has been detained in an unknown location since the generals pushed him out Wednesday. At least a dozen of his senior aides and advisers are being held in what is described as house arrest.
The arrest of Badie was a dramatic step, since even the regimes of Mubarak and his predecessors had been reluctant to move against the group's top leader. The Brotherhood was banned for most of its 83-year existence, but it has been decades since its general guide was put in a prison.
According to security officials, also arrested are Badie's predecessor as general guide, Mehdi Akef; the head of the Brotherhood's political party, Saad Katatni; one of Badie's deputies Rashad Bayoumi; and ultraconservative Salafi figure Hazem Abu Ismail, who has a considerable street following.
Authorities have also issued a wanted list for more than 200 Brotherhood members and leaders of other Islamist groups. Among them is Khairat el-Shater, another deputy of the general guide who is widely considered the most powerful figure in the Brotherhood.
The warrant against Badie and el-Shater cited suspicion they were responsible in the killing of six protesters during clashes this week at the headquarters of the Muslim Brotherhood. The deaths came when gunmen inside the building opened fire on protesters attacking the building with stones and firebombs.
Badie and el-Shater were widely believed by the opposition to be the real power in Egypt during Morsi's tenure. Badie had been staying at a villa owned by a businessman with Brotherhood links in the tourist resort city of Marsa Matruh when he was taken by security forces,
The Brotherhood's television station, Misr 25, has been taken off the air along with several TV networks run by Islamists. Morsi's critics have long accused the stations of sowing divisions among Egyptians and inciting against secularists, liberals, Christians and Shiite Muslims with their hard-line rhetoric.
In the first step toward setting up a post-Morsi leadership, the chief judge of the Supreme Constitutional Court Adly Mansour took the oath as interim president before his fellow judges at the court.
After the ceremony aired live on state TV, Mansour delivered an address praising the massive street demonstrations that led to Morsi's ouster. He hailed the youth behind the protests that began on June 30 and brought out millions around the country.
June 30 "corrected the path of the glorious revolution that took place on Jan. 25," he said, referring to the revolt against autocrat Hosni Mubarak that began Jan. 25, 2011 and led to his ouster 18 days later.
Dressed in a dark blue suit and a sky blue tie, Mansour said the rallies "brought together everyone without discrimination or division" and were an "expression of the nation's conscience and an embodiment of its hopes and ambitions."
But there was no sign of outreach to the Brotherhood in his address. He suggested Morsi's election had been tainted, saying, "I look forward to parliamentary and presidential elections held with the genuine and authentic will of the people."
The revolution, he said, must continue, so "we stop producing tyrants."
Pushing aside Morsi, army chief Gen. Abdel-Fattah el-Sissi announced Wednesday in a televised speech that the military had suspended the Islamist-drafted constitution, and that a civilian Cabinet of technocrat would run the country until new presidential elections are held. No date has been given.
Millions of anti-Morsi protesters around the country erupted in celebrations after the televised announcement by the army chief on Wednesday evening. Fireworks burst over crowds in Cairo's Tahrir Square, where men and women danced, shouting, "God is great" and "Long live Egypt."
That fact that Egypt's interim president comes from the Constitutional Court adds a symbolic sting to Morsi's ouster.
The Islamist leader and his Brotherhood backers repeatedly clashed with the judiciary, particularly the Constitutional Court, while in power, accusing the judges of being Mubarak loyalists seeking to undermine Egypt's shift to democratic rule.
The judges, meanwhile, repeatedly challenged the Brotherhood's policies and what many in Egypt considered the group's march to power. The Constitutional Court dissolved the Islamist-dominated parliament in June last year, saying it was illegally elected. It rejected a Morsi decree to reinstate the chamber.