Prime Minister Hazem el-Beblawi, who leads the military-backed government, later told journalists that authorities had no choice but to use force in the wake of recent violence.
"I feel sorry for valuable blood shed," el-Beblawi said. However, he cautioned that there will be no "reconciliation with those whose hands are stained with blood or those who hold weapons against the country's institutions."
Signaling the Brotherhood's precarious political position, Shawki said the government was considering ordering that the group be disbanded. The spokesman said the prime minister had assigned the Ministry of Social Solidarity to study the legal possibilities of dissolving the group. He didn't elaborate.
Mustafa Hegazy, a political adviser to interim President Adly Mansour, told a press conference Saturday that the current Egyptian leadership is not in a "political dispute or difference" with the Brotherhood, instead, "we are in a war against treason and some sort of terrorism."
He added that Egyptians took to the streets on June 30 — the day that led to Morsi's ouster — to revolt against "religious fascism."
The Muslim Brotherhood, founded in 1928, came to power a year ago when Morsi was elected in the country's first free presidential elections. The election came after the overthrow of autocrat Hosni Mubarak in a popular uprising in 2011.
The fundamentalist group has been banned for most of its 85-year history and repeatedly subjected to crackdowns under Mubarak's rule. While sometimes tolerated with its leaders allowed to be part of the political process, members regularly faced long bouts of imprisonment and arbitrary detentions.
Disbanding the group, experts say, would mean allowing security forces to have a zero-tolerance policy in dealing with the group's street protests, as well as going after its funding sources. That could be a serious blow to the Brotherhood, though it likely wouldn't mean an end to a group that existed underground for decades