A damning report into extremist infiltration of Birmingham schools has uncovered evidence of "coordinated, deliberate and sustained action to introduce an intolerant and aggressive Islamist ethos into some schools in the city".

The conclusion emerges from a leaked draft of a report, commissioned by the former education secretary Michael Gove and written by Peter Clarke, the former head of the Metropolitan police's counterterrorism command, which is due to be published in the next 24 hours.

Clarke said there was a "sustained and coordinated agenda to impose upon children in a number of Birmingham schools the segregationist attitudes and practices of a hardline and politicised strain of Sunni Islam".

The draft, marked as sensitive, added that: "Left unchecked, it would confine schoolchildren within an intolerant, inward-looking monoculture that would severely inhibit their participation in the life of modern Britain".

The uncompromising report may deepen community tensions in England's second city and provoke a fierce debate on whether Britain has been sufficiently muscular in efforts to expose and uproot Islamism. It will also make uncomfortable reading for Birmingham city council as it accuses local politicians and officials of ignoring evidence of extremism for years, repeatedly failing to support bullied headteachers and putting the need to soothe community tensions ahead of all else.

The report represents an explosive parting gift from Gove to the new education secretary Nicky Morgan in only her second full day in post. Touching on one of Gove's flagship reforms, Clarke calls for the Department for Education "to review the process by which schools are able to convert to academy status and become multi-academy trusts".

The former police chief said there were potentially serious problems in some academies raised by the Birmingham "Trojan horse" crisis. The draft states: "In theory, academies are accountable to the secretary of state, but in practice the accountability can almost amount to benign neglect where educational and financial performance seems to indicate everything is fine."

Ofsted has already published a report into the quality of Birmingham education after snap inspections at 21 schools revealed serious problems, leading to five schools being placed in special measures. Senior staff at Park View Educational Trust, who were identified in the Clarke report as central to the agenda, have also resigned.

In response to the Ofsted report, Birmingham local government officials and politicians accused Sir Michael Wilshaw, the chief inspector of schools, of deliberately misrepresenting problems of governance in a small number of schools by associating them with a wider threat of Islamist extremism.

Last week Mark Rogers, the chief executive of Birmingham city council, said: "We've had to deal with a national political agenda that has deliberately conflated religious conservatism with an extremist agenda that is all to do with radicalisation and violent extremism."

On Friday, Birmingham is due to publish Clarke's final report, in conjunction with its own inquiry, conducted by Ian Kershaw.

The crisis in Birmingham schools erupted in February when an anonymous letter claimed there was a "Trojan horse" conspiracy in which conservative Muslims aimed to infiltrate Birmingham schools. Although the letter is thought to be a hoax as regards the specific allegation, the broad notion of infiltration was felt to merit further investigation.

Lambasting the council, Clarke says: "There was never a serious attempt to see if there was a pattern to what was happening in school governing bodies. The council's approach has been variously described to me as appeasement and a failure in their duty of care towards their employees."

With access to internal council correspondence, he said there was "incontrovertible evidence" that senior officials and elected members of Birmingham city council were aware of the practices set out in the Trojan Horse letter as early as 2012.

Clarke's report is backed up by graphic evidence, including social media exchanges between senior staff, and disagrees with the council's previously expressed view, saying the offending ideology "manifests itself as the imposition of an aggressively separatist and intolerant agenda incompatible with full participation in a plural secular democracy".

"Rejecting not only the secular and other religions, but also other strains of Islamic belief, it goes beyond the kind of social conservatism practiced in some faith schools which may be consistent with universal human rights and respectful of other communities. It appears to be a deliberate attempt to convert secular state schools into exclusive faith schools in all but name."

Clarke said that he neither sought nor found evidence of terrorism, but there was "very clear evidence that young people are being encouraged to accept unquestionably a particular hardline strand of Sunni Islam that raises concerns about their vulnerability to radicalisation in the future".

"Essentially the ideology revealed by this investigation is an intolerant and politicised form of extreme social conservatism that claims to represent and ultimately seeks to control all Muslims. In its separatist assertions and attempts to subvert normal processes it amounts to what is often described as Islamism."

Clarke's investigation gained him access to transcripts of discussions on social media between senior figures at Park View Academy, one of the schools at the heart of the row. Heasserts: "The all-male group discussions include explicit homophobia, highly offensive comments about British service personnel, a stated ambition to increase segregation at the school, disparagement of Muslims in sectors other than their own, scepticism about the truth of reports on the murder of [soldier] Lee Rigby and the Boston bombings, and a constant undercurrent of anti-western, anti-America and anti-Israel sentiment."

A Birmingham council source said: "The performance of Birmingham in raising school attainment has recently been lauded despite the level of deprivation seen in the city."

He added: "Time and again people who have either been teachers or governors at Park View appear to be involved in behaviour at other schools that have destabilised headteachers, sometimes leading to their resignation or removal. The tactics that have been used are too similar, the individuals concerned are too closely linked and the behaviour of a few parents and governors too orchestrated for there not to be a degree of coordination behind what has happened."

Tahir Alam, the chair of governors of the Park View Trust, who is the subject of special criticism in the report, resigned earlier this week after claiming there had been a "vicious and coordinated offensive" against the trust. His fellow trustees also resigned en masse.

Timeline

December 2013 Birmingham council passes a letter to West Midlands counter-terrorism unit outlining a plot called "Operation Trojan horse", to oust headteachers and replace them with people who will run their schools on "strict Islamic principles".

7 March 2014 Counter-terrorism unit confirms it is looking into the alleged plot as details become public.

13 March Police reveal they are investigating whether the letter was a hoax connected to an employment tribunal involving a school named in the plot.

14 April The leader of Birmingham council says 25 schools in the city are under investigation following 200 complaints it has received in relation to allegations of Islamist "takeovers". Sir Albert Bore also announces that Ian Kershaw, a former headteacher with experience of leading independent inquiries, has been given a six-month contract by the council to "analyse further all Trojan horse material to enable us to see the whole picture".

15 April Michael Gove, the education secretary, appoints Peter Clarke, who served as head of the Met's counter-terrorism unit and led the investigation into the 7/7 London bombings in 2005, to examine the claims.

9 June Five of 21 schools inspected by Ofsted are judged to be inadequate and placed in special measures: Park View, Golden Hillock, Saltley, Oldknow and Nansen. Ofsted's chief inspector Sir Michael Wilshaw says "a culture of fear and intimidation" exists within the schools under investigation.

20 June The governors of Saltley resign in protest at the way their school has been treated.

15 July Trustees at Park View educational trust announce that they have quit in protest at a "coordinated and vicious" offensive led by Gove.

Haroon Siddique