Ministers are said to have concerns that more than 100 independent faith schools, most of which are Islamic, could be encouraging anti-British hatred.
According to the Daily Star, education chiefs fear that they will be unable to crack down on extremism as it is too difficult to prove it is going on.
A government source said that ‘there is a gap between what they think and know and what they can prove’.
Three schools flagged up as being “of interest” in the secret documents are run by a group which is alleged to have links to deported hate preacher Omar Bakri, the report said.
The schools, in north London and Berkshire, are controlled by the Islamic Shakhsiyah Foundation, which is reportedly been run by activists from Hizb ut-Tahrir, a hardline Islamic group Bakri was once a member of, it added.
However, the foundation said no such activists were on its board and added the Department of Education had “no concerns about extremism” in its schools.
Other faith schools said to be causing concerns include the Darul Uloom School in Birmingham.
According to the report, undercover filming at the school showed pupils allegedly being taught an extreme Islamic creed, which blasted Jews and Hindus.