Amanda Spielman, head of the non-ministerial department said new laws and powers to protect children who mostly study religious holy books such as the bible, the Sunday Times reports.
She said: "It is clear that weaknesses in current legislation allow some organisations to teach school-aged children religious texts full-time... and avoid proper scrutiny.
"Since January 2016 my inspectors have visited numerous establishments that they believe should be registered as schools. The fact that such places are able to operate and remain unregistered leaves pupils at risk."
Up to 6,000 youngsters are taught at unregistered religious centres.
Inspectors over the past 18 months have identified 286 seemingly unregistered schools across England. Of the 116 inspected, 36 have been given warning notices. Ofsted officials have been unable to gain access to the remaining.
Two years ago an unregistered Islamic school in Birmingham was closed down after inspectors found "squalid conditions, including three single mattresses covered in filthy sheets in one room and no running water in the toilet areas".
Ofsted has recommended schools for prosecution but so far, no cases have come to court. However, some have since stopped operating.
The vast majority of registered faith schools in England have a Christian faith designation, but there are also a small number of schools with other faith designations - including Muslim, Jewish and Sikh.
Spielman said she was determined to continue investigating unregistered schools and added: "We will do everything we can to make sure they comply with the law or are closed."
