He also said that two groups India blame for attacking their parliament last month - called Lashkar-e-Toiba and Jaish-e-Mohammad - would be banned.
Musharraf added that violence and terrorism have been happening in Pakistan for far too long, and that the popularity of guns in the country must come to an end.
200 arrested before the speech
Before the controversial speech Pakistani police took more than 200 members of religious groups off the streets - just in case they caused trouble.
Two other groups - Sipah-e-Sahaba and Tehrik-e-Jaffria - who are thought to be responsible for killing hundreds of people in Pakistan each year are also banned.