General Abdel-Fatah El Sissi also said that the army has no intention of seizing power, while calling on Islamists to join the political process.
General El Sissi led the July 3 coup that ousted president Mohammed Morsi. His comments came during his first appearance since a deadly crackdown on Wednesday on two encampments of Morsi supporters left hundreds dead.
General El Sissi appeared at a gathering of top military commanders and police chiefs.
Egyptian authorities have raided homes of Muslim Brotherhood members in an apparent attempt to disrupt the group ahead of mass rallies by supporters of the country's ousted president.
Under the banner of an anti-coup alliance, the Brotherhood said it will hold a demonstration in front of the Supreme Constitutional Court in southern Cairo later.
Authorities already stationed armoured vehicles and troops at the building, which could turn into another focal point of street violence.
Rallies also are planned across the country by supporters of ousted President Mohammed Morsi, deposed in a July 3 coup.
More than 800 people have been killed nationwide since Wednesday's dismantling of two encampments of Morsi supporters in Cairo - an act that sparked fierce clashes.
Some 70 police officers were killed in clashes with protesters or retaliatory attacks during the same period, according to the Interior Ministry. In an attempt to cripple the Brotherhood's protest plans, authorities carried out sweeping raids early yesterday, detaining at least 300 mid-level officials and field operatives in several cities, according to security officials and group statements.
In Egypt's second-largest city Alexandria, the Brotherhood said on its official website that security forces stormed houses of 34 officials and former lawmakers, but only arrested seven. Among those targeted was Medhat el Haddad, the brother of top Morsi aide Essam el Haddad.
In Assiut, south of Cairo, 163 of the group's officials and operatives were rounded up in different towns in the province, security officials said.
They said those arrested face charges of instigating violence and orchestrating attacks on police stations and churches.
In the city of Suez, nine people were arrested after being caught on film attacking army vehicles, burning churches and assaulting Christian-owned stores, officials said.
In ancient southern city of Luxor, more than 20 Brotherhood senior officials were detained.