Speaking on Monday at a national youth conference in Islamabad, Musharraf urged the country's young people to "launch a jihad against extremism."
"This terrorism, religious terrorism, or terrorism in the name of Islam, is un-Islamic," Musharraf said. "Suicide bombings in the name of Islam, these blasts carried out in London in the name of Islam -- is this Islam? Is this Islamic? Is this what the Holy Koran teaches us?"
Musharraf also lashed out at militant groups in Pakistan, saying they force their beliefs on others.
"There are many organizations (in Pakistan) all of which have militant names: 'Jaish' (Jaish-e-Mohammed, or Army of Mohammed), 'Sipah' (Sipah-e-Sahaba, or Soldiers of Mohammed's Companions), 'Sundullah' (Army of God)," Musharraf said. "I say there can only be one army in a country. There cannot be 15 armies. And these are the people who impose their point of view on others, by saying: 'Believe what we tell you. This is the way of Islam. Do it.'"
Musharraf said some madrasahs, or religious schools, were equally guilty of perverting Islam and imposing their ideologies on students.
Such accusations are nothing new.
During the Soviet occupation of Afghanistan in the 1980s, madrasahs had at least the tacit approval of the Pakistani government. It was in such religious schools that Pakistani intelligence service found recruits among Afghan refugees for the fight against Soviet forces.
Later, Afghan refugees used madrasahs to form a new group to take control in Afghanistan. These pupils at the madrasahs appropriately called themselves "Taliban," or students.
Now, analysts and governments point to some madrasahs in Pakistan and elsewhere as breeding the same kind of radicals, this time bent on committing acts of terrorism in countries they believe are enemies of Islam. Especially in the West the image of madrasahs is becoming synonymous with terrorist-recruitment centers.
But students at the Jamia Binoria Madrasah in Karachi disagree with this perception. Farhan Mughal, an American-Pakistani student there, said he was distraught to learn that Muslims carried out the bombings that killed 56 people in London. He says Islamic religious schools teach respect for all life.
"How come a human has a heart to do that, killing innocent people like that? Islam does not teach this, killing Muslims, and ladies and children," Mughal said. "They also have a heart. Islam even teaches how to respect animals, how to treat your animals, how to respect everything. You give your life to just help out others. This is what Islam really is. Not to take people's life for your own benefit. So it's really sad to hear this happening, and especially I don't know how these people do this."
Afzal Shaikh, another foreign student at the madrasah, said he has never heard of any teaching that would permit terrorism.
"I am studying here, I have been studying here. I haven't learned anything to do something like this," Shaikh said. "This is really disgusting."
Abdus Samad, a British citizen of Bangladeshi origin, said he could not believe the London bombers were Muslims at first, but he adds that if it were true, then it would be a heinous act for a Muslim to commit.
"First of all, I didn't believe it, that, you know, it could be Muslims who can do this kind of things," Samad said. "I went myself to the Internet cafe, and I saw the news. I still find it hard to believe that it is these people or not who bombed it (London). It might be a conspiracy or something, I don't know. But if it is (Muslims) it is very shameful. It is very shameful and it is a disgrace."
Madrasahs are responsible for producing the next generation of Islamic clergy, but they are also centers of learning not only about Islam but philosophy, mathematics, and foreign languages.
While the majority of madrasahs are seen as teaching students to behave humanely, Musharraf said yesterday that a few have strayed from their purpose and now promote their own personal views as part of the curriculum.
Musharraf said these are the ones that represent a danger to others.