The expulsion rate at one of the Government's flagship city academy schools was more than ten times the national average in its first year.
King's Academy, in Middlesbrough, ejected 26 out of 1,034 pupils in 2003-4, a rate of 2.51 per cent, according to The Times Educational Supplement.
The average figure for England was 0.23 per cent but the academy, which is sponsored by millionaire car dealer and evangelical Christian Sir Peter Vardy, said children excluded themselves if they broke the rules.
The Government has put the academy programme at the heart of its five-year plan for education; ministers say they want 200 to open by 2010.
Independent schools that are not allowed to charge fees, city academies are intended to replace comprehensives with histories of failure.
Academies are publicly funded for the most part, although private sponsors contribute up to £2m towards start-up costs.
Sir Peter first sponsored Emmanuel City Technology College, in Gateshead, which was embroiled in a row after it emerged that pupils were taught the creationist view of history, which says the Genesis version of the origins of the universe is true, alongside the national science curriculum.
He set up the Emmanuel Schools Foundation to sponsor seven academies in the North.
The third, Trinity Academy in Doncaster, is due to open next year.
A spokeswoman for the Foundation said that King's Academy was a very special school in that it replaced three comprehensives that had to be closed.
She said: ''We have a very clear discipline policy and it is something that parents and students sign up to.
''They know that there are consequences for misbehaviour. That could be anything from persistent misbehaviour in the classroom to bringing drugs into the school.
''Children exclude themselves if they break the rules. It is as simple as that.''
She confirmed that, in the past, Emmanuel's website carried a document which posed the question of whether or not divine intervention stopped Hitler invading England during the Second World War.
The website was redesigned earlier this year and no longer contains the material.
But the spokeswoman said that the document, entitled Christianity and the curriculum, underlined the need to use a ''frame of reference in which God is sovereign''.
The document continued: ''In this context, it becomes important to peruse why Hitler paused at the English Channel when an immediate invasion could have led to a swift victory.
''Could it be that God was calling a halt to this march of evil?''
The spokeswoman said: ''What we've always said about the Foundation is the schools we sponsor have a Christian-based ethos.
''All kinds of issues are debated and all faiths are studied by the children but they are never told to believe one thing or another.
''They are always left to make up their own minds.
''The material doesn't represent what is being taught on a day-to-day basis.''
The popularity of the Foundation's schools was demonstrated by the fact that they were over-subscribed, she added.
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