All foreigners are to be removed from Pakistan's more than 10,000 Quranic schools, Musharraf said on Friday.
No new visas will be issued to non-Pakistanis wishing to study in the seminaries and prayer schools. The ban will apply to holders of dual nationality.
"An ordinance to this effect will be adopted in the next coming days," General Musharraf said, as part of new rules requiring all seminaries to register with the government by the end of the year.
British Prime Minister Tony Blair has urged Pakistan to move against what it deems extremist and radical schools (madrassas) following news that some of the London 7 July bombers had recently visited the South Asian country.
Continuation of the crackdown
Musharraf vowed to continue a crackdown on hardliners he ordered last week, in which security forces said they had rounded up more than 600 suspected militants and Islamic clerics.
Pakistanis say they are being unfairly targeted and have recently taken to the streets in protest.
Mirajul Huda speaks at a protest
over mass arrests in Karachi
Musharraf said that, do date, no one had been arrested who was directly related to the London bombings.
"The investigation is going on. It's a little premature to draw a conclusion. It's a very tedious job."
The president, who has banned 10 groups considered extremist, said the raids had aimed not at rounding up large numbers of people but at catching the leaders of the Islamic radical underground.
"I don't want to arrest the workers," he told a group of foreign correspondents. "I want the leaders of the banned groups. I'm not impressed by figures. We want to get all of the bigwigs."
Musharraf pledged to enforce a ban on anti-Western speeches at mosques or on audio recordings.
Asked about the seriousness of the arrest campaign, Musharraf said: "I have never done anything not seriously. I don't bluff. I do act with realism. I am realistic, not idealistic. I am very, extremely, serious."
Madrassas offer free religious education and board for more than one million Pakistani children, especially in areas neglected by state education services. Some have been targeted for preaching hatred against the West.
Some schools were set up as military training sites during the 1979 to 1989 US-backed war against the Soviet occupation in neighbouring Afghanistan.
"I want the leaders of the banned groups. I'm not impressed by figures. We want to get all of the bigwigs"
Under the registration drive, the tribal North West Frontier Province had registered 720 religious seminaries, provincial law and parliamentary affairs minister Malik Zafar Azam said late on Thursday.
As part of the arrests, Pakistani security services this week arrested Hashim Qadeer, a fugitive suspect in the 2002 murder of Wall Street Journal reporter Daniel Pearl.
US President George Bush later on Thursday phoned Musharraf to discuss the "war on terrorism" and regional issues, said White House spokesman Scott McClellan without giving further details.
Security sources believe Osama bin Laden may still be hiding in western Pakistan, but Musharraf said this week his forces had dismembered al-Qaida and broken its communications structure.
Pakistani military near the
Pakistan shares a 2400km (1,500-mile) border with Afghanistan in the rugged and lawless mountain areas of the North West Frontier Province and Baluchistan, tribal regions which were for long beyond the reach of the central government.
Almost daily violence rocks the region, where 70,000 Pakistani troops are hunting Taliban and al-Qaida linked insurgents, who use remote mountain hideouts to stage cross-border raids on US and Afghan government targets.
In another step set to tighten border security, Pakistan says it will start issuing machine-readable visas with photographs within six to eight weeks to foreigners.
Machine-readable Pakistani passports, recognised by the United States and Britain, have already been issued to Pakistani nationals in Saudi Arabia and Dubai, said senior immigration official Brigadier Khalid Habib.