The meeting in Islamabad on Monday will focus on amendments that President General Pervez Musharraf made last week to a law on registration of welfare.
Maulana Sharif Hazarvi, who runs Jamia Rabbania school, or madrassa, in Islamabad, said the amended law requires Muslim schools to identify their sources of income in their annual audit reports to the government.
"If we give names of people who may have given donations, police will go after them and harass them," Hazarvi said.
There are more than 10,000 schools in Pakistan with an estimated one million students.
Most of the schools are funded by private donations. Also, some schools are said to be affiliated to religious political parties.
Schooling for the poor
President Pervez Musharraf has
demanded schools be registered
Religious schools in Pakistan also offer schooling for the poor who cannot afford a formal education.
In recent weeks, Musharraf has renewed his demand for the schools to register with the government and include certain subjects in their syllabi.
He has also told the schools to expel all foreign students, who number about 1400.
Musharraf's call came after investigators said two of the four suspects in the 7 July bombings that killed the bombers and 52 other people in London may have been to schools in Pakistan.
Officials have confirmed the suspects visited Pakistan, but there is no evidence that suggests they went to any of these schools.