Michael Gove's decision to appoint a former anti-terror chief to investigate allegations of a hardline Islamist takeover plot at a number of Birmingham schools was "singularly inept", a teachers' leader has said.

Mary Bousted accused the Education Secretary of making a "politically-motivated" appointment, adding that the move has "badly misfired".

Peter Clarke, who served as head of the Metropolitan Police's counter-terrorism unit, was announced yesterday as the Government's new education commissioner, with responsibility to investigate the Birmingham allegations.

But the decision swiftly came in for heavy criticism, with one top police officer saying it was a "desperately unfortunate appointment" that will be misinterpreted by some people.

The Department for Education (DfE) has insisted it is confident that Mr Clarke's background makes him the right man for the job.

Voicing her own concerns about Mr Clarke's appointment, Dr Bousted, who is general secretary of the Association of Teachers and Lecturers, questioned why the Education Secretary had established a separate inquiry.

"The local authority is investigating this issue. Why not let the local authority investigate the issue?" she said.

"Why ratchet up the tension? And why make such a politically-motivated appointment, which complicates the issue, rather than throws any light on the issue?"

"This can only be Michael Gove acting in a politically-motivated manner with no real desire to find out the truth of the matter, but to make political capital."

She added: "Michael Gove's choice is singularly inept and, in my view, it was a politically-motivated appointment which has badly misfired."

Dr Bousted said she would not be commenting on the allegations before they had been fully investigated.

West Midlands chief constable Chris Sims criticised Mr Gove's move yesterday, saying: ''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 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) has 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''.

Mr Gove has said 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."

In total, 25 schools are now under investigation over the alleged hardline Muslim plot to force out governors and headteachers.

Allegations of a coordinated move by a small group of hardliners, dubbed Operation Trojan Horse, first emerged when an anonymous letter apparently setting out a blueprint for the takeover of governing bodies was leaked to the media.

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.

Ofsted has since been sent in to 15 schools after Mr Gove asked for inspections to be carried out.

Among those known to have been inspected as a result are the city's Saltley School and Adderley Primary School, both in Saltley, and Regents Park Community Primary School, in Small Heath.

In addition, Ofsted has also been into the classrooms at Nansen Primary School, Saltley; Golden Hillock School, in Sparkhill; and Park View Academy, in Alum Rock - all part of the Park View Educational Trust, alleged to be the focus of the claimed takeover plot.

The results of these inspections are expected to 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 alleged a colleague praised during a pupil assembly 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".

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.

On Monday, the city council announced it was appointing chief adviser and former headteacher Ian Kershaw on a six-month contract to sift through the 200 complaints received by the local authority since Trojan Horse came to light.

It has also convened an investigative group chaired by Stephen Rimmer, a Home Office director general and troubleshooter currently seconded to the West Midlands, to review Mr Kershaw's findings and publish a report on the issues by May.

Council leader Sir Albert Bore expressed "frustration" at the fact they were having to deal with a two-tier system of local authority-controlled schools and academies - answering only to the DfE - which meant establishing even basic facts such as who was on any particular academy's board of governors had become a task in itself.