The Brotherhood repeatedly has denied government claims that it uses or condones violence. Instead, they accuse the government of trying to stymie the group as part of its crackdown against it.
Ibrahim Elsayed, a member of the Brotherhood's political arm, the Freedom and Justice Party, dismissed the accusations by Ibrahim as "security illusions."
"He didn't prove the involvement of any member of the Brotherhood in particular in any of the attacks he mentioned," Elsayed said. "This is an immature attempt to embellish the image of the interior ministry at a time it is shedding the blood of Egyptians."
Ibrahim said five senior militants were detained from two pro-Morsi sit-ins which authorities broke up violently in August, including senior members of Islamic Jihad and Gamaa Islamiyya.
The two groups were responsible for some of the worst attacks in Egypt in the 1980s and 1990s, but many of their leaders have since given up violence and formed political parties after the ouster of longtime autocrat Hosni Mubarak. The groups were allies of Morsi and the Brotherhood.
Ibrahim accused sit-in participants of stockpiling weapons. He said other militants arrested were released from prison by Morsi's government. He said his forces have arrested more than 60 militants accused of various attacks, including the assassination of a senior security official who was in charge of monitoring Islamist groups. He said the forces also seized weapons and ammunitions intended for use in operations his forces foiled.
Also among those arrested was an Egyptian who coordinated operations and finances between a Libyan militant group and others in Egypt, Ibrahim said. A wanted militant that plotted a foiled assassination attempt on Ibrahim in September had trained in Syria, the minister said.
Ibrahim said the government was working to freeze Brotherhood assets to stop money from sponsoring violence or further protests.
He also warned that his forces will deal "firmly and with force" with any protests they deem not peaceful or which block main streets "regardless of the losses for me or for them."
Morsi allies refuse to recognize Egypt's military-backed interim authorities and organize near-daily protests against them. Some demonstrations descend into violence. They plan mass demonstrations Sunday to remember the day police violently cleared the sit-ins.