Representatives of an alliance of Pakistani madrassas, or Islamic Seminaries, who met in Islamabad on Monday, have decided not to register.
Under a new order decreed by President Pervez Musharraf last month, all madrassas are required to register by the end of this year or close down.
An alliance spokesman says the new law is discriminatory because it does not require other religious seminaries to register. The madrassas also argue that donors will stop giving them money if they release their names, as required by the new law.
Authorities say they suspect some of the madrassas have been breeding grounds for Islamist militants. President Musharraf decreed the new law after revelations that at least one of the four bombers in the July seventh attacks on London had visited a Pakistani madrassa just before the attack.