General Pervez Musharraf vows to crush extremists throughout Pakistan.
However, he said the government had no plans to demolish the mosque, and it was being renovated to be reopened for prayers on Friday.
Pakistani army commandoes stormed the complex and adjoining Jamia Hafsa seminary for women on July 10 after those running a Taliban-style movement from the complex refused to surrender.
The government said 102 people were killed in eight days of fighting when security forces stormed the complex.
After the assault, President Pervez Musharraf, an important ally of the United States in its “war on terror”, vowed not to allow mosques or madrasas to be misused.