Key individuals were "promoting and encouraging certain Islamic principles" in Birmingham classrooms amid poor oversight from education chiefs, a city council investigation into the alleged "Trojan Horse" takeover plot has found.
However, the Birmingham City Council inquiry carried out by Ian Kershaw also concluded: "There is no evidence of a conspiracy to promote an anti-British agenda, violent extremism or radicalisation in schools in east Birmingham."
But his report's conclusions differ to those of a leaked draft of former Metropolitan Police counter-terrorism chief Peter Clarke's own investigation, commissioned by the Department for Education (DfE), which found a "sustained, co-ordinated agenda to impose segregationist attitudes and practices of a hardline , politicised strain of Sunni Islam".
While Mr Clarke and Mr Kershaw looked at much of the same evidence both men have arrived at different findings - a state of affairs criticised as "regrettable and unhelpful" by the National Association of Head Teachers union (NAHT).
The "Trojan Horse" allegations first surfaced in a letter leaked to the press in March claiming a clique of hardline Muslims governors were taking over governing boards and removing uncooperative headteachers.
Mr Kershaw's 151-page report found governors, deputy and acting headteachers, trustees and parents involved in a pattern of behaviour "moving between schools in the area".
It concluded "elements" of the so-called "Trojan Horse" five-step plan to seize control of governing boards were present in 13 schools, including the three academies of Park View Educational Trust (PVET) - at the centre of the allegations.
He added: "The evidence shows individuals have been seeking to promote and encourage Islamic principles in the schools with which they are involved, by seeking to introduce Islamic collective worship, or raising objections to elements of the school curriculum that are viewed as anti-Islamic."
Mr Kershaw concluded: "There is little express evidence to which I can point of a systematic plot or co-ordinated plan to take over schools serving students of a predominantly Muslim faith or background."
Mr Kershaw's report said the problems had been allowed to run "unchecked" due to what he branded "weaknesses in the system and poor oversight of governance" mainly by the city council, but also by Ofsted, the Education Funding Agency and the DfE.
Sir Albert Bore, council leader, welcomed the report's 21 recommendations but said he would not comment on the two report's differing conclusions.
He said: "Ian Kershaw was quite clear that he needed to verify what was being said - and I'm pleased he had.
"There's therefore conclusions (in Kershaw's report) I can more readily accept and promote."
But Russell Hobby, NAHT general secretary, said: "The discrepancies between the two are regrettable and unhelpful."
He added that part of the problem was that the inquiries had used different definitions of "extremism".
Mr Hobby criticised the council inquiry's terms of reference as "too narrow" which "prevented them from taking the evidence that they needed", pointing out the lack of anonymity extended to people wishing to give evidence to Mr Kershaw may have had an impact.
"We cannot fully support the conclusions reached by the city council's review into the 'Trojan Horse' allegations," he added, but said the union would continue working with the council on all the issues.
In the leaked report published in The Guardian, Mr Clarke concluded: "The agenda, but not the tactics, involved stem from an international movement to increase the role of Islam in education."
The report findings further stated: "Left unchecked, it would confine schoolchildren within an intolerant, inward-looking monoculture that would severely inhibit their participation in the life of modern Britain."
Mr Clarke's report has also taken account of a conversation between individuals on social media WhatsApp, which the council received but could not verify.
Sir Albert said: "The WhatsApp information came on a CD anonymously."
Both reports have been heavily critical of governance failings and of the city council's inability to tackle the problem of errant governing boards over a period of many months and years.
Mr Kershaw's report uncovered evidence as far back as 2007 "there were already signs of some of the behaviour" carrying on.
Mark Rogers, the council's chief executive, said the council is now commissioning another report to uncover how many school staff may have been wrongly forced out by the unscrupulous governors.
Meanwhile, eight local education authority governors have so far been removed from nine schools according to the council, and more could be "barred".
Sir Albert said: "We must acknowledge the council's failings.
"The report has highlighted areas were we have either taken no action, were too slow, or have simply done the wrong thing.
"The report states this has often been because of the risk of being seen as racist or Islamaphobic."
Mr Kershaw's report also laid some of the blame on the city council's "significant gaps in oversight" of governance by "resource restraints".
He was also critical of council staff operating "in silos" where different departments failed to share information.
The report also said it was "not possible to discern a relationship" between the council, Ofsted or the DfE in sharing critical data.
Shadow education secretary Tristram Hunt said: "There is a dangerous lack of oversight in David Cameron's schools system and the results of this are being played out in Birmingham. Peter Clarke is right to describe the Government's approach as one of 'benign neglect' - ministers failed to act on warnings they were given in 2010.
Standards are being damaged and schools exposed to risk because of an ideological refusal to give local areas new powers to oversee schools.
"Labour has proposed new local directors of school standards to support and challenge schools to improve and to root out problems before they set in."
The DfE said: "Peter Clarke has been asked by the Department for Education to make a full inquiry into Birmingham schools and the background behind many of the broader allegations in the Trojan Horse letter.
"He will report back shortly and it is absolutely vital this investigation is carried out impartially, without pre-judgment.
"It would be inappropriate to comment further at this stage."