The DfE said it had taken action because of continuing failings by the school.
When Ohr Torah was inspected in July 2018, it had 59 boys aged from 11 to 16 on its roll - already 20 more than approved by the DfE under the school’s registration terms. Last year the number rose to 87.
In a follow-up inspection report last March, Ofsted said pupils did not have enough opportunity to develop skills in English and were not learning enough about other faiths and cultures.
Ofsted said at the time that "parents were not willing to permit pupils to talk to the inspector about British values, other faiths and cultures or the protected characteristics".
Protected characteristics - which refer to groups of people protected from discrimination under equality law - include sexual orientation and gender reassignment.