"We will not stand by silently watching the destruction of the country and the people or the torching the nation and terrorising the citizens," said powerful Defence Minister General Abdel-Fatah el-Sisi.
In a speech aired on state television, Gen Sisi said the army has no intention of seizing power, but instead "have the honour to protect the people's will - which is much dearer (than) ruling Egypt."
The Brotherhood has been protesting against Morsi's ouster. Several rallies by the Islamists against the military-backed government have turned violent resulting in deaths of over 800 people, mostly Brotherhood supporters.
"We have given many chances... To end the crisis peacefully," Gen Sisi said and asked Morsi's supporters to take part in the political process instead of confrontations and destroying the Egyptian state.
His speech came after security forces carried out a series of raids across Egypt and detained over 300 mid-level Brotherhood leaders, aimed at preventing the Islamists from staging anti-government rallies.
His remarks came ahead of an emergency meeting of the military-backed interim government which will decide the fate of the Brotherhood, which was banned under previous Hosni Mubarak regime.
