There is "disturbing" evidence that people with a "shared ideology" were trying to gain control of governing bodies in Birmingham, says Education Secretary Nicky Morgan.
She was responding to the Trojan horse report from former counter-terror chief Peter Clarke into allegations of a hardline Muslim take-over of schools.
Mr Clarke found evidence of an "aggressive Islamist agenda".
Ms Morgan highlighted "intolerant" messages between school staff.
Teachers could face misconduct inquiries, she told the House of Commons, after Mr Clarke's report found a social media group called the "Park View Brotherhood" used by male senior staff at Park View School.
Mr Clarke's report said this included "grossly intolerant" messages.
He said the social media messages included "explicit homophobia; highly offensive comments about British service personnel; a stated ambition to increase segregation in the school; disparagement of strands of Islam; scepticism about the truth of reports of the murder of Lee Rigby and the Boston bombings; and a constant undercurrent of anti-western, anti-American and anti-Israeli sentiment".
Ms Morgan also announced that there would be an education commissioner for Birmingham, who would report to the education secretary and to Birmingham City Council's chief executive.
There will be a wider review of the "governance culture of the council", which would report by the end of the year.
The education secretary warned that the council's inability to intervene reflected a "culture of not wanting to address difficult problems where there is a risk of accusations of racism or Islamophobia".
Rather than supporting head teachers under pressure, she said the council could be responsible for helping them to be "eased out".
Sir Albert Bore, leader of the city council, welcomed the creation of an education commissioner and said the authority was "making progress".
"In addition, we are already working on a number of key areas such as strengthening governor appointments and training and our whistle-blowing process and reporting, as well as continuing our work in reviewing our relationship with all schools," said Sir Albert.
Labour's Tristram Hunt said that the "chickens had come home to roost" - blaming the problems on the lack of oversight in the academy system.
Mr Hunt told MPs that the "free market policy" in running schools had "fomented the crisis in Birmingham".
Mr Clarke had delivered the findings of a report commissioned by the Department for Education.
Much of the report had already been leaked - and representatives of schools facing allegations claimed they had faced a "co-ordinated and vicious" attack from the government.
The inquiry found no evidence of extremism, said Mr Clarke, but "there are a number of people in a position of influence who either espouse, or sympathise with or fail to challenge extremist views".
"I have established that there is a group of associated individuals in positions of influence in schools and governing bodies who have, over quite a considerable time, looked to introduce what could be described as an aggressive Islamist agenda into some schools, very few schools, in Birmingham," Mr Clarke told the BBC.
"The report gives a description of a number of practices that really have no place in state, non-faith schools. There's clearly been a wish to introduce what has been described as a conservative religious agenda into those schools.
"There is a group of people of like mind, who are well known to each other, who have been working together for a number of years - and they have deliberately sought to bring those practices into the schools."
The report raises concerns about the lack of intervention by the local council, which he says was too sensitive to "community cohesion".
"It's quite clear that Birmingham City Council either knew or suspected that these things were happening for a considerable period of time, but didn't do enough to stop it," said Mr Clarke.
He also warned that there needed to be a review of the accountability of academies. These are autonomous state schools - and are now the most typical secondary school - but he highlighted concerns about a lack of oversight.
Concerns about schools highlighted in the report included Friday prayers broadcast through schools but stopped during Ofsted visits, banning Christmas celebrations and complaints that female staff were not treated equally.
This is the latest in a series of reports triggered by an anonymous and unverified letter which claimed that there was a "Trojan horse" conspiracy to take over governing bodies and create a school culture more sympathetic to their hardline Muslim religious ethos.
Mr Clarke's investigation says the significant question was not whether this was a "genuine" letter, but whether "the events and behaviours described have actually happened".
"It quickly became apparent to me that although there are some factual inaccuracies in the letter, there is also a great deal that is true, some of which had not previously been in the public domain," says Mr Clarke's report.
His inquiry found evidence that concerns had already been raised, including an internal council email about claims that head teachers had been "hounded out... as a result of organised community action focused on a group of Muslim governors".
Mr Clarke's report highlighted a "disconcerting pattern" in the schools, including nepotism in staff appointments, bullying of senior teachers, a "strategy of harassment to oust the head teacher" and the "reinforcement of Muslim identity to the exclusion or disparagement of others".
Ofsted chief Sir Michael Wilshaw, delivering his own findings last month, said there had been a "culture of fear and intimidation" in which head teachers had been undermined by governing bodies.
He told MPs that head teachers had described how they had been bullied by governors wanting to intervene in the day to day running of the school.
Inspectors had carried out a wave of inspections in Birmingham, with five schools being put into special measures.
Birmingham City Council's inquiry had found "no evidence of a conspiracy to promote an anti-British agenda, violent extremism or radicalisation in schools".
But the council's report said that the patterns outlined to destabilise schools in the "Trojan horse" letter were "present in a large number of the schools considered part of the investigation".