Head teachers have voiced "serious concerns" over the way in which at least six Birmingham schools have been apparently been put under pressure by hardline Islamicists.
Leaders of the National Association of Head Teachers said heads were being put under pressure by "organised groups" taking over governing bodies and putting pressure on heads to change the character of schools to adopt Islamic practices.
In addition, they revealed, teachers and support staff were being appointed on the grounds of their faith rather than their teaching skills.
As a result, children were missing out on their entitlement to a broad school curriculum, with a question mark being put over whether all were receiving equal entitlement to dance, drama and PE lessons.
Russell Hobby, general secretary of the NAHT, added that he did not believe the problem was confined just to Birmingham. "I think we're talking about a small number of schools throughout the country," he added.
The NAHT's intervention is the first time heads or teachers have indicated the extent of the problem, which was sparked off by a "Trojan Horse" letter alleging schools were being forced to adopt hardline Islamic practices such as segregating boys and girls for lessons, and that heads were put under pressure to go along with them.
In his speech to his annual conference in Birmingham on Sunday, Mr Hobby will add: "A tight network of religious leaders of the Islamic faith has made a concerted effort to get involved in the running of schools and to strengthen the power of governing bodies to have a dominant influence in shaping the character of local schools.
"It is not clear that they have done anything wrong just by doing this... however, in some instances, this influence has gradually crossed the boundaries of good governance and deprived some students of their entitlements in terms of knowledge and education.
"It has also crossed the line in terms of employment law in order to exert this influence by getting people of the right religious views appointed."
Mr Hobby said the NAHT had offered support to 30 head teachers as a result of the allegations, and found itself involved in detailed casework to help heads in a dozen schools. In six cases, they had found "serious concerns".
He will add: "Schools should not be places for indoctrination in any creed or ideology, political or religious."
The NAHT said the schools concerned were a mixture of primary and secondary - and included both council-run schools and academies. In a statement, it added: "In a small number of cases, the association believes the actions [of governors] may have broken the principles of governance, contravened good employment practices and risk eroding the basic entitlement of children to a good education."
Under Education Secretary Michael Gove's reforms, Mr Hobby added, schools had lost some of the local monitoring and oversight of their performance, and strong boundaries had to be set determining what was permissible and what was not.
Mr Hobby said the NAHT believed the original letter was a "fake" designed to draw attention to the problem. "We don't believed these allegations are a source of panic but neither do we believe they are a source for comfort," he added.
At least four separate inquiries have been set up as a result of the allegations: Mr Gove has appointed former head of the Metropolitan Police's anti-terrorism unit Peter Clarke to hold an inquiry, education standards watchdog Ofsted has carried out inspections of 21 schools, the Education Funding Agency, responsible for school funding, has carried out an investigation, as has Birmingham City Council. West Midlands police are also investigating the affair.
Because of strict rules covering Government announcements during any election period, it is now thought unlikely that any of the reports will be published before the European elections on 22 May. Chief schools inspector Sir Michael Wilshaw has told inspectors they must carry out more work at some of the schools before the reports are published early in June.