Michael Gove is under fire for his decision to appoint a former anti-terror chief to investigate allegations of a hardline Islamist takeover plot at a number of Birmingham schools.
The Education Secretary announced that Peter Clarke, who served as head of the Metropolitan Police's counter-terrorism unit, is to become education commissioner, with responsibility to investigate the allegations.
The move swiftly came under increasingly heavy fire, with one top police officer saying it is a "desperately unfortunate appointment" that will be misinterpreted by some people.
The Department for Education has insisted it is confident that Mr Clarke's background makes him the right man for the job.
Mr Clarke's role will be to conduct an investigation to fully understand the situation and work with Birmingham City Council to "analyse evidence of extremist infiltration in both academies and council-run schools", the Department for Education (DfE) said.
It added that Mr Clarke has substantial experience in leading high-level investigations and his appointment means that the allegations can be examined in a "professional and dispassionate manner".
But West Midlands chief constable Chris Sims said: "This is a desperately unfortunate appointment. Peter Clarke has many qualities but people will inevitably draw unwarranted conclusions from his former role as national co-ordinator for counter-terrorism."
He later said he had great professional regard for Mr Clarke, but added: "There is no doubt that some people will misinterpret his previous role and see the current issues being faced within schools in Birmingham as being a counter-terrorism issue, which for sure it isn't."
Mr Sims said that the Birmingham allegations remained primarily linked to issues of school governance.
"It's an issue about cohesion and the way social cohesion plays out into schools, but it certainly isn't, from anything we know at the moment, an issue about counter-terrorism," he said.
"I think it will make people in east Birmingham concerned that judgments are being made about what lies behind this issue and I suppose the reassurance we must give is that no such judgments are being made by West Midlands Police. We are supporting the work that the council is doing but the support is around the governance issue within schools and principally issues of social cohesion."
West Midlands elected police and crime commissioner, Labour's Bob Jones, said he shared Mr Sims's concerns.
Mr Gove has said that he is "extremely concerned" about the allegations that have been made, and while Ofsted is inspecting a number of schools of concern, more action was needed.
"These allegations need either to be substantiated and firm action taken, or to be shown to be baseless," he said.
"We cannot allow uncertainty for parents or pupils to persist.
"That is why I am appointing a commissioner to oversee this work. Peter Clarke brings a wealth of relevant skills and experience, and is very well placed to lead a fair and thorough assessment of the evidence, and report back to me. We expect he will work closely with Birmingham City Council."
A Department for Education spokeswoman later said: "We are confident that Peter Clarke's background makes him exactly the right appointment for this important job.
"He has long experience of leading sensitive investigations, and has earned a reputation for thoroughness, integrity and independence. He has worked for many years with diverse communities and in collaboration with a wide range of partners.
"The Secretary of State believes that Mr Clarke's track record, drive and professionalism will mean parents in Birmingham can be confident that the truth of what has happened will be uncovered."
Mr Clarke's appointment comes the day after it was disclosed that 25 schools are now under investigation over the alleged hardline Muslim plot to force out governors and headteachers.
Birmingham City Council has already announced it is appointing a new chief adviser, Ian Kershaw, managing director of Northern Education, to directly handle at least 200 complaints received in relation to the Operation Trojan Horse allegations focusing on schools in the city. It is also setting up a review group.
Concerns over how some of the city's 430 schools were being run first emerged when an anonymous letter known as Operation Trojan Horse was leaked, claiming a small but radical group of Muslims were pursuing their own agenda in the classrooms, with uncooperative headteachers and governors forced out.
The unsigned and undated document also 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.
Since the letter came to light, anonymous whistle-blowers have claimed that boys and girls were segregated in classrooms and assemblies, sex education was banned, and non-Muslim staff bullied, and in one case it was alleged that the teachings of a firebrand al Qaida-linked Muslim preacher were praised to pupils.
Birmingham City Council leader Sir Albert Bore has said that West Midlands Police are still looking into the authorship of the document.
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.
Among further claims which have since come to light, one former anonymous staff member at Park View Academy in Alum Rock alleged a colleague had praised in an assembly the firebrand al-Qaida-linked Muslim cleric Anwar al-Awlaki, who was killed by a US drone strike in Yemen in 2011.
The school trustees have firmly denied all the claims, branding the allegations "a witch hunt", while pointing to very good academic results among its pupils.
Birmingham Ladywood MP Shabana Mahmood described Mr Clarke's appointment as a "deeply provocative" and disappointing move by the Education Secretary.
The Labour MP said: "I am a Muslim member of parliament for Birmingham. I was born here. I grew up here I went to Small Heath School.
"The idea that the way that one looks into these allegations of governance and bullying in a transparent, judgment-free way is to appoint a counter-terrorism expert is quite simply shocking.
"What would have been much more appropriate was an adviser-led process with someone appointed jointly by the DfE and Birmingham City Council, as suggested by myself and every other member of parliament for Birmingham."