"Egypt will not be governed by another Khomeini," the Supreme Council of the Armed Forces said after a three-hour meeting with newspaper editors-in-chief and MENA.
"The Supreme Council of the Armed Forces will not allow extremist factions to control Egypt," Deputy Defence Minister Mohammed Mokhtar al-Mella told the journalists on Monday.
The military also reiterated its commitment to transfer power to civilian rule after legislative and presidential elections, and to respect freedom of expression.
It "expressed the hope that the Egypt of tomorrow will be democratic and modern", MENA reported.
Mubarak in February transferred his powers to the military, which has committed itself to handing the reins to civilian rule after a parliamentary election due in September.
A presidential election is due "one or two months" after that.