"We will not allow madrassas to be misused for extremism, hatred being projected in our society."
No new visas will be issued to foreigners wishing to study in the schools.
But the BBC's Aamer Ahmed Khan says it is not clear what effect these measures will have on extremism as the more militant students work at unregulated madrassas that have survived previous crackdowns.
An ordinance would be adopted "in the coming days" on the new move, Gen Musharraf said.
He also told journalists that action would be taken against any of the madrassas that did not register with the authorities.
The president had previously announced all schools must register before December.
Pakistani forces have detained hundreds of clerics and suspected militants since President Musharraf announced a new crackdown on 15 July.
British Prime Minister Tony Blair called on Pakistan to curb extremists and radical madrassas in the wake of the London bombings of 7 July.
The Jamia Manzoorul Islam madrassa in Lahore denies links to a London bomber
Gen Musharraf said on Friday that no arrests in Pakistan were directly related to the bombings.
"The investigation is going on. It's a little premature to draw a conclusion. It's a very tedious job," he said.
The president also vowed to crack down on anti-Western hate speeches in mosques or in recordings.
In a recent visit to a Lahore madrassa, our correspondent Aamer Ahmed Khan found foreign students visibly uncomfortable with the links being drawn by the media between terrorism and religious education.
The students said they were there simply to learn and were "more disappointed than angry" at the terror links.
It is estimated that there are around 20,000 madrassas in Pakistan.
According to the Pakistani newspaper, The News, there are around 1.7m students at the institutions, mainly from poor rural families.
The number of foreigners dropped sharply after the 11 September attacks in the US.
New rules after the attacks obliged foreigners to state in their visa applications where they planned to study. The visas became invalid if they left the madrassa.
President Pervez Musharraf's latest crackdown on extremism, outlined in his July address to the nation, appears to have been aimed in two directions, inwards to his fellow Pakistanis and also to the rest of the world.
Most of his time was taken up with painting a picture of the country's contemporary realities - not all of which may be visible from the outside.
Perhaps what is most significant was the subtext that strongly suggests that there is little Pakistan can do to tackle its problem of extremism without active assistance and support from the outside world.
One significant departure from President Musharraf's earlier references to extremism relates to his candid admission of Pakistan's "direct or indirect" linkages to the scourge of extremism.
"No matter where something happens, we end up being directly or indirectly involved," he said. Involved, he said, and not blamed.
"It turns out that they [extremists] have either visited Pakistan or passed through it on their way to Afghanistan."
This is a marked departure from the country's existing policy of flatly denying any linkage with Islamist extremism.
MUSHARRAF'S NEW MEASURES Banned groups not allowed to operate under new names No public displays of unauthorised weapons Clampdown on inflammatory material, including audio, video tapes and their publishers and distributors Militant groups not allowed to collect funds Monitoring hate sermons from mosques All madrassas registered by December 2005
Gen Musharraf then elaborated on the extremism-related realities within the country.
Between 20,000 to 30,000 Muslim militants, he said, flocked to Pakistan from all over the world during the US-backed war against the Soviets in Afghanistan through the 1980s.
He said all their finances and logistics were routed through Pakistan.
"Where are they now?" he asked. "Not all could have stayed on in Afghanistan."
The president let the question hang there.
If one were to assume - even if purely for the sake of argument - that many of these subsequently found their base in Pakistan, then what was the environment that greeted them?
According to President Musharraf, the fallout from the Afghan war has divided Pakistani society into roughly three categories.
There are those who subscribe to what he called orthodox Islamic thought. Then there are those that are enlightened and educated and finally there is the vast majority who have been left terribly confused about Islam by the Afghan war.
Musharraf gets his message across
The president said that the orthodox group had for 26 years been raising funds, recruiting manpower, providing military training and spreading hate literature in aid of the extremists.
At times the extremists also draw support from Pakistan's mainstream religious parties, he said.
It is hard to avoid concluding from his remarks that the country has been providing an ideal sanctuary for Islamic extremists.
Not many are likely to find fault with the picture of Pakistan painted by General Musharraf in his address to the nation.
As the head of the Pakistan army - an institution credited with crafting and carrying Pakistan's pro-jihad policy in Afghanistan - few know more about what goes on in Pakistan than the army chief.
What is important is how the world reacts to the problems outlined by the president.
His own prescription is multi-pronged.
Gen Musharraf wants a far more dynamic role for the Organisation of Islamic Conference in the affairs of the Muslim world.
He also wants active assistance and support from the West - not only in tackling extremism but also in helping many Muslim nations in the developing world out of their vicious cycles of public poverty.
But lastly, and perhaps most importantly, President Musharraf wants the West to give a deep think to the festering disputes that involve the Muslim world.
The subtext of all that he said seemed to indicate his conviction that only after the West and the Muslim world are able to resolve their disputes can the latest measures he has announced against extremism be expected to bear fruit. ---------------
For Pakistan's powerful military and the rugged Pashtun tribesmen, the South Waziristan region, near the border with Afghanistan, is a virtual war zone.
The vast mountainous region remains out of bound for non-locals. Journalists have been barred from the area, and the main town of Wana looks like a military garrison.
Local residents are getting caught in the crossfire
Almost daily skirmishes, landmine explosions, and use of heavy artillery and occasional aerial bombing, makes it a deadly conflict zone.
The latest military offensive in which air force bombers and gunship helicopters pounded an alleged training camp of suspected al-Qaeda militants, has resulted in heavy casualties. And it has taken the conflict to an area that until now had remained relatively peaceful.
This was the third time in recent weeks that the military bombed suspected militant hideouts. It has given a new and a more serious dimension to the security operation within the country.
Until now, aerial bombing has never been used to crush an armed insurgency in the country.
No end in sight
The military may not have suffered any serious casualties in the latest offensive, largely because it used air power and long-range rockets. But since the present conflict began in March, scores of soldiers have been killed, including officers.
Dozens of foreign and local militants have also been killed. But it is becoming increasingly clear that the victims of this undeclared war are the local tribesmen and their families, who have been caught in the crossfire.
In some ways it suggests that the military's assessments about the fighting strength of the militants, and the risk to civilians, were wrong.
So what will be the outcome of this bloody conflict, which does not seem to have an immediate end? No-one seems to have an answer.
The military offensive had been part of the overall war against al-Qaeda.
The US-led forces have largely been operating across the border in Afghanistan, and Islamabad admits, have also been assisting the Pakistani troops in surveillance and communication.
The co-ordinated effort is largely aimed at capturing top al-Qaeda leaders Osama Bin Laden and Ayman al-Zawahri. The men, and many of their close associates, are widely believed to be hiding in and perhaps operating out of the area.
Tribal groups angry
Since the start of operation, the military authorities have firmly established that a large number of Uzbek, Chechen and Arab militants were in the area.
Battle-hardened tribesmen have taken the military action as an attack on their sovereignty, and have been putting up stiff resistance.
Most parts of the semi-autonomous tribal region have traditionally resisted the presence of foreign forces, including Pakistani troops.
It was in July 2002 that Pakistani troops, for the first time in 55 years, entered the Tirah Valley in Khyber tribal agency. Soon they were in Shawal valley of North Waziristan, and later in South Waziristan.
This was made possible after long negotiations with various tribes, who reluctantly agreed to allow the military's presence on the assurance that it would bring in funds and development work.
But once the military action started in South Waziristan a number of Waziri sub-tribes took it as an attempt to subjugate them.
Attempts to persuade them into handing over the foreign militants failed, and with an apparently mishandling by the authorities, the security campaign against suspected al-Qaeda militants turned into an undeclared war between the Pakistani military and the rebel tribesmen.
Some analysts say it is a no-win situation for the Pakistani troops. They cannot abandon the operation half-way, but are now having to use bombers and gunship helicopters against what was earlier described as a "handful of foreign militants and some local miscreants".
Relations between the authorities and local tribesmen have deteriorated to such an extent that the troops may remain bogged down long after all the foreign militants have been eliminated or flushed out of the region.