But some experts question whether Musharraf is willing or able to reform the most radical Islamic boarding schools, where clerics encourage militancy.
Musharraf's latest madrasah-reform pledge followed the deadly raid to wrest Islamabad's Red Mosque from militant Islamists fortified inside.
"The madrasah [at the Red Mosque] was turned into a fort for the preparation for war," he said in a televised speech after the raid. "So much so that terrorist elements had been given sanctuary here. Our resolve is that in the future, we will not allow any mosque or madrasah to be misused like [the Red Mosque] or the Jamia Hafsa [madrasah]."
Musharraf's dependency on political support from conservative mullahs has led some experts to say they don't expect to see substantial reforms at Pakistan's most militant madrasahs anytime soon.
Robert Templer, the Asia program director for the International Crisis Group, oversaw research for a report in March about Pakistan's madrasahs. Templer tells RFE/RL that the Red Mosque crisis highlights the failure of Musharraf's previous reform pledges to bring about changes to the country's most radical madrasahs -- those with ties to Pakistan's Inter-Services Intelligence (ISI) agency that had spawned Afghanistan's Taliban movement.
"There are a small number of very extreme madrasahs like the Red Mosque that need to be closed down," Templer says. "These are institutes that are fostering sectarian violence. They've caused thousands of deaths in the past decades. They are training militants. They are preaching hatred. They are a source of dangerous publications, tape recordings, preachings. These need to be closed down. I don't think any modern state could tolerate essentially vigilante armies in its own territory operating in this way. And I don't think these madrasahs are 'reformable' as such. They need to be closed down."
Still, despite the urgency of a situation, Templer doesn't have much confidence in Musharraf's renewed pledge.
"I don't think it will go far at all. We've seen Musharraf on a number of occasions, going back to January of 2002, say that he is going to reform the madrasah system," Templer says. "And yet absolutely nothing has been done. He tends to announce a big new policy, and then it gets watered down, and then, finally, it just disappears altogether. And I believe that is what is going to happen again. We've already seen some conciliatory statements from the government. We've already started to see a little bit of push back from the madrasah union in particular. I don't think the government is going to want to take on the madrasahs, and I don't think they are going to do much to reform this system or the overall education system."
Musharraf is in a difficult position. He depends on conservative clerics for domestic political support in parts of Balochistan and the Northwest Frontier Province close to Pakistan's border with Afghanistan.
But Musharraf also depends on the United States for military support in the counterterrorism effort. Since the terrorist attacks of September 11, 2001, he has replaced many pro-Islamist ISI commanders.
His cooperation with the United States in the hunt for Al-Qaeda, however, has angered conservative Islamists in the border regions. The deployment of Pakistani troops in the semi-autonomous tribal regions has fueled further tension between Musharraf and conservative Islamists.
Attorney Abdul Latif Afridi is an ethnic Pashtun tribal leader from Pakistan's Northwest Frontier Province and president of the Peshawar High Court Bar Association.
Afridi and others say madrasah militancy began to prosper in Pakistan when Islamic radicals were recruited by the ISI to join the anti-Soviet resistance in Afghanistan.
Karachi's Jamia Benoria seminary in mid-2006
Afridi says the ISI continued to encourage Islamic radicals after the Soviet defeat in Afghanistan -- giving them funds and weapons and then exporting militants to Afghanistan and Kashmir.
In an interview with RFE/RL's Radio Free Afghanistan, Afridi alleged that Pakistan now trains Islamic militants and sends them into Afghanistan.
Afridi also says that in Pakistan's tribal areas, radical religious students and clerics continue to arm themselves instead of preaching about "peace, security, moderation, and reconciliation."
"You can imagine how many weapons there are at other madrasahs in the tribal areas and how strong they have become there," Afridi says.
Templer agrees that the links between Pakistan's military and radical mullahs are clear. He says that helps explain why there has been little progress under a madrasah-reform scheme unveiled by Musharraf in 2002.
Madrasahs And Militancy
Templer also says the Red Mosque crisis proves that students at the most radical madrasahs continue to receive military training.
"Nobody knows for sure how many madrasahs there are in Pakistan, but figures range from 10,000 up to about 30,000," Templer says. "The vast majority of them are simply religious schools that often provide the only education that is available for poor people. And the vast majority are entirely benign, although they don't necessarily equip students well for a modern economy. The problem lies really in a very small number of them -- a handful of madrasahs in some of the main cities, in the Northwest Frontier Province, and in some of the tribal areas along the border with Afghanistan. And these are madrasahs that are run by radical clerics that have taken on strong positions against other forms of Islam, against the West, and are often linked into jihadi groups -- particularly those operating in Afghanistan and Kashmir."
Rasul Baksh Rais is a political columnist and analyst for "The Daily Times" newspaper in Pakistan. A professor of political science at Lahore University of Management Sciences, Rais says most madrasahs in Pakistan do not want to be associated with militancy.
"We can see how the madrasahs have responded to the [Red Mosque] crisis," Rais says. "The federation of religious institutions has cut the two madrasahs [at the Red Mosque complex] from their [accreditation] list. They cut them off the list and they did not give them any legitimacy or any recognition. We don't see any uprisings at any major madrasahs throughout the country. We can expect Pervez Musharraf to be very harsh on [radical] madrasahs. I don't mean that he is going to be [hard on all madrasahs]. But he needs to, and also the state of Pakistan needs to be very harsh on any madrasahs where there are militants."
Templer says the real victims of militant madrasahs are poor youths who have no other educational opportunities.
"Overall, the madrasah system needs to be updated so that it provides a better education for students," Templer says. "Secular education needs to be improved as well. And that should be the focus of policymaking, in my view. It is the secular education that needs to be improved. If people in Pakistan are given a choice, they will send their children to the better-run schools -- no matter what their religious convictions are. Wealthy and well-educated Pakistanis do not go to madrasahs. They go to a whole host of other schools, but certainly not madrasahs. What is needed is a state system that provides opportunities for far more people than it currently does."
(Contributors to this report include Ayesha Khan in Prague and RFE/RL's Radio Free Afghanistan)