The Department for Education (DfE) is understood to be investigating the Association of Muslim Schools UK (AMS-UK) and the Bridge Schools Inspectorate (BSI) amid claims that some of their inspectors support fundamentalist Islamic beliefs, The Sunday Times reported.
The newspaper had reported the so-called Trojan Horse plot to take over school curriculum in Birmingham - Britain's second largest city - last month.
Birmingham has a large Muslim population - nearly 22 per cent, according to the 2011 census.
Peter Clarke, the former Scotland Yard anti-terrorism chief who was appointed special commissioner by UK education secretary Michael Gove last month, is also expected to look into the two bodies.
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News of the latest inquiries came days after Gove flagged the likelihood of both state and private schools being inspected by UK schools inspectorate Ofsted.
At present, Ofsted's remit is predominantly limited to state-funded schools.
Ofsted is expected to give a clean bill of health to two of the 18 schools across Birmingham that it is investigating over alleged bids to impose Islamic practices.
It has been asked to inspect three more primary schools in the city, bringing the total to 21.