The Bishop of Bradford has been called in to broker top level talks over deep-seated problems which have emerged as part of the shake-up of the district's schools.
In one area, anger has arisen after scores of children failed to get places at a new flagship Church of England secondary school.
Parents claim they have been misled over the admissions' policy at Immanuel College, in Thackley, and are demanding it is changed.
Meanwhile, in another row, parents and governors at Thornbury primary are protesting that their planned new school will not be big enough, forcing children to be bussed off-site for sports lessons.
Angry Ravenscliffe families say they believed the £12 million Immanuel College would be a direct replacement for Eccleshill Upper - which closed last summer as a result of the re-structuring of the three-tier system.
But more than 60 children have failed to get into Immanuel this September as a result of a decision to give community places to children living nearest the school.
Nearby Hanson and Laisterdyke schools are also full and have turned families away leaving many children being offered Carlton Bolling College, Undercliffe, which has about 180 spare places.
But in many cases the school, which can offer cutting-edge technology and was opened this month as a £600,000 city learning centre, is being snubbed by families who had not put it down as a preferred choice.
The council's executive committee member for education, Councillor David Ward said the parents in Ravenscliffe, Thorpe Edge and Fagley areas were incensed over the problems they now faced and he felt they had been misled when the schools reorganisation plans were being discussed.
Coun Ward said: "I am not surprised they are angry and the fault doesn't lie with Immanuel or the other schools.
"It lies with some former politicians who certainly gave the impression that their children would be going to this new school. There is strong feeling and I am very, very sorry for them."
"Carlton Bolling may be near, but it is not in the same neighbourhood. They feel they have nothing in common with it. A lot of this is territorial, The people who did the schools re-organisation plotted it on maps without regard for social harmony.
"I have asked officers to look at whether Carlton Bolling can be a viable school without the children from Fagley and Ravenscliffe and look at the feasibility of another small secondary school."
Immanuel admitted more than a hundred 14 and 15-year-olds from Eccleshill Upper as a "one-off" when it opened last September to give them continuity at a crucial time in their education.
But that has sparked a further protest because brothers and sisters admitted in future will only be those living closest to Immanuel.
In a letter to Coun Ward, the Bishop, the Right Reverend David Smith, says it has become clear in talks between Carlton Bolling and Immanuel on admissions policy that issues and implications in the Bradford north have become much wider than just their schools.
The two schools have asked the Bishop to convene a meeting with the education representatives from the Conservative, Labour and Liberal Democrat groups to discuss the situation.
Coun Ward said Immanuel was situated in a densely-populated area and although he disagreed with its admissions policy, the local authority had no control because it was a church-controlled school.
But the Archdeacon of Bradford, the Venerable Guy Wilkinson, chairman of the governors at Immanuel, said places went to children who lived nearest and it was a neighbourhood school. He said: "This isn't a problem caused by admission and not a matter created by Immanuel.
"It is a problem created by people who are no longer councillors who gave them the impression they had a right to go to Immanuel.
"We hope all the schools can get together and end up with a policy which can satisfy everybody.
"Immanuel is not selective. It is a local school. We wish it to be a locally-based school with a Christian ethos."
He said there would normally be 240 admission places each September - half for children with church connections, and half for the community.
But he said the numbers could vary and this year there had only been 40 children filling church criteria, with the rest going to the community.
He added there may sometimes be fewer applications from the immediate neighbourhood and those from further away might be successful.
The Archdeacon said a high proportion of the children at Immanuel were already from Eccleshill because they were given automatic admission last September.
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