Yemeni authorities have ordered the closure of all unregistered religious schools.
The country has also commissioned a review of what is taught in class, to ensure students receive what it terms a moderate interpretation of Islam.
The move comes as fighting continues in the north of Yemen between government forces and rebels.
Correspondents say the order to close the schools could affect hundreds of private institutions across the nation.
The rebels are led by Hussein Badr al-Din al-Huthi, a member of the minority Zaidi Shia sect who runs a religious school in Saada province.
The government accuses him of using Friday prayers to organise violent anti-American protests.
Reports say the violence in Saada province has left 60 people dead including 15 soldiers.
Pressure
On the official level, Yemen has been a strong supporter of Washington's "war on terror".
Like Pakistan and Saudi Arabia, its neighbour to the north, Sanaa has come under pressure to reform its education system.
Al-Qaeda is widely believed to operate in parts of Yemen where the central government's influence is weaker.
In October 2000 the US naval vessel USS Cole was damaged in a suicide attack in the Yemeni port of Aden which was subsequently blamed on al-Qaeda. Seventeen US personnel were killed.
In February 2002 Yemen expelled more than 100 foreign Islamic scholars, including British and French nationals, in a crackdown on terror and suspected al-Qaeda members.
Later the same year, the supertanker Limburg was badly damaged in attack, blamed on al-Qaeda, off the Yemeni coast.