Concerns are being raised with the Government over the performance of two super-schools, opened as a town's new hope for the future.
Protests have been made to Schools Minister David Miliband about the City and Unity academies in Middlesbrough which between them have excluded more than 40 pupils from classes this year.
Complaints have been raised by Labour Coun Paul Thompson, executive member for education with Middlesbrough Council.
While standards in literacy, maths and science across the town's secondary schools are in line with national levels, "the two city academies have performed worse than the others,'' states a damning report to go before Middlesbrough Council.
Prime Minister Tony Blair unveiled the idea of city academies in 2000 as the new generation of schools for the future, aimed at raising education standards in deprived areas.
Their introduction met with opposition from some teachers who forecast that the new schools would be divisive - and cream off the best pupils.
With more than 40 pupils excluded between the two Middlesbrough academies - some of them special needs youngsters - council resources have been "severely over stretched.''
Local education chiefs are meeting the heads of the town's secondary schools to find places for the expelled children.
Coun Thompson said yesterday: "I have spoken to David Miliband about this issue. I felt I had to raise this issue and I have written to him on the subject.
"The exclusions have caused us problems across the town. We have to continue the education of the kids, we don't have the luxury of just abandoning them.
"I am disappointed. Academies were set up in educationally challenged areas, so you are going to get challenging kids. Over two thirds of children excluded in Middlesbrough come from just two schools.
The principals of the two academies could not be contacted for comment at the weekend. But the Northern Echo understands they will be asked by the council's education scrutiny committee to give account if, as feared, the academies' GCSE results are poor.
City academies are part of the Labour Government's "big picture'' for education, with plans have 200 up and running by the year 2010. But Government overtures to have more built at Middlesbrough are expected to be resisted.
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