Pakistani officials say some of the madrasahs teach intolerance to other faiths and even other creeds of Islam.
They worry that some students, including hundreds who come to Pakistan from other parts of the Muslim world, could become easy recruits for extremist groups opposing Western and Western-backed governments worldwide.
As part of the crackdown, Pakistani President Pervez Musharraf last month ordered that the schools to register by the end of the year or face being closed down.
But the madrasahs are fighting back.
The Alliance of the Organizations of Religious Schools Pakistan, an umbrella organization representing thousands of seminaries, vowed on 12 September to defy the order.
"The amendment for the registration of madrasahs is unacceptable to us because it is discriminatory," said Maulana Abdul Maalik, a member of the alliance. "These conditions have not been imposed on any school, or college, or any other organization. They have only been imposed on madrasahs."
Authorities have distributed forms to madrasahs urging them to refrain from teaching that promotes militancy or sectarian hatred.
The forms also seek information on numbers of teachers and students, and details of their income and expenditures.
Clerics who run Islamic schools say they fear that individuals who give donations to their institutions will be harassed by the government if it gets their names.
Maalik told Reuters Television that the new requirements compromise the independence of the madrasahs.
"All these conditions will bring the freedom and independence of the madrasahs to an end," he said. "Our first and last duty is to preserve the freedom of the madrasahs.”
Analysts say the government will have to tread carefully on the issue because Pakistan’s madrasahs provide food, lodging, and at least a rudimentary education to close to a million boys from poor Pakistani families.
Under his drive to rein in Islamist militancy, Musharraf has also ordered Islamic schools to expel their 1,400 foreign students, without setting any deadline.
Foreign students in madrasahs began sitting annual examinations this week with anxiety, fearing to be sent home without qualifying as "alims," or Islamic scholars.
Farhan Moghul, a New Yorker who is studying at a madrassa in the southern city of Karachi, is one of them.
He told Reuters Television that he hoped the government will reconsider its strategy.
"Next year is my last year, which is the most important year of my education," he said. "And I planned to finish it next year in this madrasah. And we plead again hopefully, and we ask that [Pakistani officials] give us permission to come back because we should complete our last year of education."
Pakistan saw a spectacular rise in the number of madrasahs in the 1980s, when the schools were recruiting volunteers fighting communist forces in neighboring Afghanistan.
Some madrasahs later supplied recruits for the Taliban regime, which was toppled by a U.S.-led coalition in late 2001.
More recently, at least one of the bombers in the 7 July attacks on London was believed to have visited madrasahs in Pakistan.
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