Asked by the Saudi-owned daily, Al-sharq al-Awsat, how the government dealt with Islamist teachers in Egyptian schools, Baha al-Din on Tuesday replied: "Thousands of extremist teachers were removed."
The minister said his decision to remove them was based on reports from the security services and from supervisors in his ministry as well as on complaints from students' parents.
He added that he "removes a teacher immediately" once he determines he or she is bent on challenging national policy, without saying whether the teachers were removed permanently, according to the London-based daily.
On 1 March, Baha al-Din said Egypt would take lessons from no one over reforming its school books in a bid to promote religious tolerance and stamp out sources of terror.
The comments published by the government newspaper Al-Missa appeared as the United States has stepped up its campaign for reform in Arab countries, including calls to amend school textbooks deemed intolerant.
In response to charges from Islamists, the minister said "rumours that we have withdrawn from school texts Quranic verses and the sayings of the prophet Muhammad, and that we marginalise Islamic history, are totally unfounded."