Ofsted inspectors have been sent into 15 schools to investigate an alleged 'plot' by hardline Muslims to force out uncooperative headteachers and governors.
The schools, which are all in Birmingham, have faced accusations of extremism and radicalisation after an anonymous letter was leaked.
The document, which is unsigned and undated but which was sent to local authorities and teaching unions as far back as last year, claimed to have caused "a great amount of organised disruption" in the city crediting the plan with forcing a change of leadership at four schools.
The move by Ofsted comes after Education Secretary Michael Gove asked for inspections to be carried out.
The Department for Education (DfE) said it was vital the investigations were "carried out impartially" and said it would be inappropriate to comment further at this stage.
A parallel investigation is also being carried out by Birmingham City Council, and one academy school has had its financial arrangements reviewed by the Education Funding Agency.
The council last week announced a freeze on the recruitment of local authority school governors across Birmingham stating that the system was "not fit for purpose".
An update on the progress of the city council's inquiry is expected this week.
The allegations detailed in the Trojan Horse letter focus on the Park View Educational Trust, which runs three schools in the city - all of which have been subjected to snap Ofsted inspections in recent weeks.
It is understood the results of these inspections will be published after Easter.
Anonymous whistle-blowers, including former teachers, have also come forward since the Trojan Horse claims hit the media, making accusations about the segregation of boys and girls in classes and assemblies, a ban on sex education, and bullying of non-Muslim staff.
One former staff member at Park View Academy in Alum Rock alleged a colleague had in an assembly praised the firebrand al Qaida-linked Muslim cleric Anwar al-Awlaki - he was killed by a US drone strike in Yemen in 2011.
However, the school trustees have firmly denied all the claims, branding the allegations "a witch-hunt".
The school's governors have also pointed to the turnaround in pupils' GCSE results in recent years, with three quarters of students completing their studies having gained at least five grade A* to C qualifications, including maths and English in 2013.
Separately, West Midlands Police said at the beginning of March - after scrutinising the Trojan Horse letter - it was reopening a fraud inquiry into allegations first made by staff members at another school in the city in January 2013, but ruled out any wider anti-extremist or counter-terror investigation into the claims made in the document.
All of the city's MPs recently wrote a letter to Mr Gove calling for a full inquiry into the issues in order to settle the matter and help restore confidence in the schools identified in the alleged plot.
A DfE spokesperson said: "The allegations made in relation to some schools in Birmingham are very serious and we are investigating all evidence put to us in conjunction with Ofsted, Birmingham City Council and the police.
"It is absolutely vital these investigations are carried out impartially, without prejudgement.
"It would be inappropriate to comment further at this stage."
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