The private school, which teaches 140 children aged under 11, and holds classes for over-16s and adults, is run by cleric Mufti Zubair Dudha of the Deobandi sect, which is believed to run half of the mosques and Islamic schools in the UK.
The Department for Education said: “While it would be inappropriate to comment on the specific investigations, we are clear that extremism has no place in our society and we are determined to protect children from it.”
Mr Dudha told Sky News: "It saddens me greatly that certain extracts from our publications have been taken and misrepresented to link the Academy with extremism.
"We fully believe in the importance and need of integration whilst being able to practise our faith."