Twenty-five schools are being investigated in connection with an alleged plot by conservative Muslims to force out headteachers and governors.
A new chief advisor is now being appointed by Birmingham City Council to handle the at least 200 complaints received in relation to Operation Trojan Horse after an unsigned, undated document was sent to the council and teaching unions last year.
It apparently set out a blueprint for seizing control of the governing bodies of schools, and forcing out those who do not agree. It claimed to have forced a change of leadership at four schools.
Whistleblowers - including former staff - have made a number of allegations against schools in Birmingham since the accusations came to light, including one claim the teachings of an al-Qaeda-linked preacher were praised in front of pupils.
Other complaints include the alleged segregation of boys and girls in lessons and assemblies, a ban on sex education and bullying of non-Muslim staff.
Deputy Prime Minister Nick Clegg said he was "very, very concerned about allegations that taxpayer-funded schools have become vehicles of particular ideologies".
"I have always supported faith schools but the best faith schools use their religious identity as engines of integration rather than silos of segregation," he added.
The council's investigation, running alongside a separate inquiry by the Department for Education (DfE), is due to initially report back in May.
At a briefing, councillors said the 25 schools being investigated in Birmingham included primaries, secondaries, community schools and academies. Fifteen of the schools have so far been inspected by Ofsted.
Birmingham City Council also confirmed that it was in contact with authorities in Bradford and Manchester who had been experiencing "similar" issues.
Sir Albert Bore, the council leader, told Sky News: "It's about the day-to-day practices in schools we're concerned about, it's also the impact these allegations are having on community cohesion in Birmingham.
"Certainly there is a feeling amongst the Muslim community in Birmingham that there is a 'hue and cry' on at the present moment in time, we have to be concerned about that, just as we're concerned about what is actually happening in the schools themselves."
Councillor Brigid Jones, cabinet member for children and family services, said: "It's a whole range of allegations, some concerning the governance of schools, some concerning the quality of teaching and everything in between, covering a period of around 20 years.
"I do worry about the children in those schools, we know they've felt increasing community tensions as a result of it and a lot of people have felt marginalised and stigmatised. This is something we don't want whatsoever."
A spokesperson for West Midlands Police said there is no official investigation but they were being kept informed of developments.
Khalid Mahmood, Birmingham Perry Barr, MP told Sky News: "I believe fundamentally there has been a serious bid by a very small minority trying to get under the radar against the wishes of the mainstream Muslim community."
Mr Mahmood said he had been told of the "bullying and harassment" of senior teaching staff and governors at some of the schools involved.
He said: "What they were trying to do is change the theological beliefs of the majority of the Muslim community into a more hardline belief for young people coming through, and if you put all the schools together you're talking somewhere in the region of 3-4,000 children and that in a community of young people coming though is huge.
"What I've said to them is be honest and transparent. If you want to do this then apply for a free school, say this is your ethos, this is what you want to do, and this is the way to deal with it."
Ladywood MP Shabana Mahmood said she and her fellow Birmingham parliamentarians had written to the Government asking for it to lead any investigation, as some of the schools involved were academies and not under local authority control.
She also claimed Ofsted could have questions to answer.
"I'm in regular contact with schools in my constituency and the first I have heard is when allegations were made in the media," Ms Mahmood told Sky News.
"I recognise disclosures have been made elsewhere and that's why I think we need a proper process. I think there are questions here for Ofsted to answer if it's found that some of these schools have got failing governance procedures and there have been attempts at takeovers.
"Some of these schools have been judged outstanding recently - and it begs the question, if this is found to be true, why these schools were found to be outstanding when there are problems there."
Children in the city have been set two pieces of homework over the summer. One is entitled "What does a good inclusive education in Birmingham look like?", the other poses the question: "What does a safe and resilient citizen of the future look like?"
A Department for Education 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 pre-judgment. It would be inappropriate to comment further at this stage."