A raft of reforms to school accountability, including an education commissioner for Birmingham, inspections of city academy chains and new oversight of school governors, were announced on Tuesday by the education secretary in response to a damning report into extremist infiltration of schools.

Nicky Morgan said that in the future teachers would be sacked without appeal if it was proven that they have failed to protect pupils or promote British values by exposing children to extremist speakers.

The moves followed the publication on Tuesday of a report showing there had been a co-ordinated attempt to take over a small group of Birmingham schools by a group of politicised Sunni Muslim extremists.

The report, written by Peter Clarke, the former head of counter-terrorism at the Met, was leaked to the Guardian last week. It calls for a review of the way in which schools become academies or academy trusts, a proposal not taken up by Morgan.

Clarke said he found an "intolerant and aggressive" Islamist ethos in some Birmingham schools brought about by governors intent on promoting an ultra-conservative version of their faith. That ethos included homophobia, sexism, antipathy to other forms of Islam and in one case denial that Private Lee Rigby had been killed by Islamic extremists.

The new schools commissioner for Birmingham will oversee reforms to the way school governors are selected and operate, as well as ensure that all children are properly prepared for life in the modern world. The appointment has been welcomed by Birmingham council.

Morgan also announced that the outgoing head of the home civil service, Sir Bob Kershaw, will conduct a review of Birmingham council's corporate culture.

The council is now Labour controlled, but was run by an alliance of Tories and Liberal Democrats until March 2012. The new council's political leadership has admitted, in hindsight, it put community cohesion before rooting out the problems in some schools, including systematic bullying of teachers resisting attempts to narrow the culture and curriculum of state schools.

The current Birmingham chief executive has been fiercely critical of the former education secretary Michael Gove and the Ofsted chief inspector Sir Michael Wilshaw.

Morgan said: "What Peter Clarke found is disturbing. His report sets out compelling evidence of a determined effort by people with a shared ideology to gain control of the governing bodies of a small number of schools in Birmingham. Teachers have said they fear children are learning to be intolerant of difference and diversity. Instead of enjoying a broadening and enriching experience in school, young people are having their horizons narrowed and are being denied the opportunity to flourish in a modern multicultural Britain."

One of the schools at the centre of the row, Oldknow Academy, was told it will have its funding agreement terminated by the Department for Education. In a letter to the academy trust's board, the schools minister, Lord Nash, said Oldknow had failed to show it had taken adequate steps to improve. A further letter from the minister states the DfE will revisit the school in October, to scrutinise its action plan.

Clarke also criticised unnamed professional bodies – believed to be a reference to the National Union of Teachers and the NASUWT – for putting to one side consideration of "the systematic problems" their Birmingham members faced in their relationships with school governors.

He also said the two unions, unlike the National Association of Head Teachers, had refused to assist his inquiry proactively. These professional bodies, he said, "have been active in securing compromise agreements for their members where professional agreements have broken down, but consideration of the more systematic problems affecting their members appear to have been put to one side". Both unions, in statements, strongly condemned intolerance, but continued to claim the criticisms of the schools had been exaggerated.

In the Commons, Les Lawrence, the former lead education councillor in Birmingham, a Conservative, was one of four people named under parliamentary privilege by Khalid Mahmood, the Labour MP for Birmingham Perry Barr, who accused them of colluding "with this huge tragedy of keeping these schools in a position they should not have been in", and failing to listen to parents, governors and teachers.

In her statement, Morgan made two policy announcements that might have not been made by her predecessor Gove, and one notable shift in tone.

Shadow education secretary Tristram Hunt said her appointment of a school commissioner for Birmingham was a welcome shift and broadly in line with proposals he had made jointly with the former education secretary David Blunkett for a localised tier of accountability responsible for driving up school standards. Hunt has been concerned that the proliferation of academies has left the Department for Education in charge of thousands of schools.

Gove had already created eight regional school commissioners, including one for the West Midlands.

Morgan said that below these eight commissioners, appointed by the Department for Education, will be elected headteacher boards, which will consist of outstanding headteachers. She said she hoped these bodies would be the places unhappy teachers could turn in the future if they have complaints about local school governors or the response of the local council. Morgan also for the first time said her department needed to look at Ofsted being empowered to inspect academy chains, a power Wilshaw has sought.

Morgan also spurned an opportunity to follow Gove in his rhetorical demands for tougher action to deal with Islamist extremism. She was asked by a Tory backbencher Rob Wilson: "What approach does she favour in attempting to combat extremism – simply beating back the crocodiles that come too close to the boat, or draining the swamp?" Morgan said simply: "I believe in looking forward and learning lessons." Liam Byrne, the Birmingham MP for Hodge Hill, was one of many Labour MPs to blame the former education secretary for making longstanding problems in some local schools worse. He said: "Over the last six months, I've been appalled by the way some in government decided to use this as a political football, a pawn in their culture wars, and a chance to attack our city's proud Muslim community. That's why I'm so glad Michael Gove is no longer education secretary.

In Birmingham, governors representing three academies run by Park View Educational Trust resigned en masse last week, claiming to be victims of a Department for Education witch-hunt.

Key findings

• There was a coordinated, deliberate and sustained action to introduce an intolerant and aggressive Islamic ethos into a few schools in Birmingham.

• There was no terrorism, radicalisation or violent extremism in the schools of concern, but there was clear evidence of a number of people, associated with each other and in positions of influence in schools and governing bodies, who espouse, endorse or fail to challenge extremist views.

• Birmingham city council was aware of the practices and behaviour that were outlined in the Trojan horse letter long before the letter surfaced.

• People who have been either teachers or governors at Park View school appear to be involved in behaviours at other schools that have destabilised headteachers, sometimes leading to their resignation or removal.

• The tactics used are too similar, the individuals concerned too closely linked, and the behaviour of a few parents and governors too orchestrated for there not to be a degree of coordination and organisation behind what has happened.

• An all-male group discussion called the Park View Brotherhood, initiated by the acting principal of Park View school, contained messages that displayed 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-US and anti-Israeli sentiment.

• Teachers in the city fear children at some of the schools of concern are learning to be intolerant of difference and diversity. There is evidence that this is the case both inside and outside school, such as on school trips.

• Young people, instead of enjoying a broadening and enriching experience in school, are having their horizons narrowed and are not being equipped to flourish in the diverse environments of further education, the workplace or any environment outside predominantly Muslim communities.

• The very clear evidence that young people are being encouraged to accept unquestioningly a particular hardline strand of Sunni Islam raises concerns about their vulnerability to radicalisation in the future.

• The council has not supported headteachers faced with aggressive and inappropriate behaviour by governors.

• The sheer number and diversity of people who made allegations about the schools disproves the idea that those claiming to witness extreme behaviours were simply disaffected teachers and headteachers.

• Parents do not have the confidence to argue against the articulate and forceful activists who seek to impose their views, for fear of being branded as disloyal to their faith or their community.

Rowena Mason