The move against 14 of the Brotherhood's leaders came two weeks after an estimated tens of millions of protesters thronged streets throughout the country to demand the resignation of former President Mohammed Morsi, who the Brotherhood backed.
Three days later, the military leadership ousted Mr. Morsi, installed a top judge as president and detained 650 Brotherhood members, Brotherhood lawyer Ali Kamel said. Of those, 550 have since been released on bail, but Mr. Kamel added that at least 56 top officials remain in a high-security detention.
Mr. Morsi was not seen since. The military has said he is in army custody for his own protection.
The legal maneuvers against the Brothers came as Egypt's interim leadership moved forward with political appointments that also appeared aimed at further isolating the Brothers and their supporters.
Chief among them was the swearing in of Mohamed ElBaradei, a leading liberal figure who has faced open hostility from Islamists, as vice president in charge of foreign affairs. He will be joined by Nabil Fahmy, a trenchant critic of the Morsi administration and a former Egyptian ambassador to the U.S. Mr. Fahmy was named on Sunday as the interim foreign minister.
The swift legal moves have raised concerns in Egypt and abroad that Egyptian judges, whose mostly secularist thinking put them squarely at odds with the powerful Islamist group, may be planning a punitive crackdown on the Brotherhood. Many Egyptians have said they worry that further alienating the Brothers and their conservative Islamist allies could delay political reconciliation and shake the foundations of Egypt's new government even before they are built.
Egypt's new president, Adly Mansour, has repeatedly called for reconciliation between the secularists who streamed through Egyptian streets in recent weeks and the Islamists, who recently controlled almost every facet of the Egyptian state.