Protests broke out across the Middle East on Friday, with demonstrations in Egypt, Syria, Jordan and Lebanon, demanding an immediate halt for the Israeli digging near the holy site.
Israel denies the repair work and accompanying excavations will come anywhere near the compound, known as the Temple Mount to Jews and the Noble Sanctuary to Muslims.
Egyptian anti-riot police scuffled with demonstrators in Cairo and prevented worshippers from getting inside the Al-Azhar mosque, the Sunni Arab world's most powerful institution. Demonstrators held a smaller protests in Alexandria and other Egyptian cities.
Since late last year, police have detained at least 140 Brotherhood members, including its number 3 leader, Khayrat el-Shater, whose case was one of 40 who have been referred to a military court. State owned media have recently intensified their campaign against the Muslim Brotherhood.
The banned but tolerated movement is Egypt's largest opposition group, after having won 88 out of the 454 parliament seats in the 2005 legislative elections.