Mohammed Ibrahim's comments were the first detailed account offered by a senior Egyptian official to back claims that the Brotherhood, the group of ousted Islamist President Mohammed Morsi, is responsible for attacks against security, government institutions and the country's Coptic minority. However, he didn't provide proof to back up his claims.
The wave of violence intensified after the government carried out a bloody crackdown on Morsi supporters that killed hundreds in August.
Ibrahim accused the Brotherhood of enlisting the help of militant groups linked to al-Qaida and Palestinian extremist groups operating in the Gaza Strip following the popular protests against Morsi that started on June 30. The military forced Morsi out of office days later.
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The Brotherhood offered no immediate reaction today to the minister's claims.
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.