As the second academy to open in Norfolk, City Academy Norwich has been something of a flagship for the movement.
The school, which replaced Earlham High in 2009, has a state-of-the-art multi-million pound building, but, for the past two years, its GCSE results have fallen well below the government's minimum targets.
Now, newly-published accounts for 2013-14 have revealed that concerns about the school's academic performance have forced its sponsor to put plans to expand its portfolio of schools on hold, and at the same time the school is having to pay back hundreds of thousands of pounds in over-paid grants.
The school is adamant its long-term future is secure, and its financial issues did not contribute to recent disappointing exam results.
In the academy's first year, a grant to help with the conversion process, from the Young People's Learning Agency which was then responsible for funding further education for 16-19 year olds, was overpaid.
A spokesman for the school said: 'The reason City Academy Norwich is having to repay £479,000 of this grant is the Department for Education miscalculated the amount that should have been granted and came back at later date asking for repayment.'
And last year, the school was hit by a demand to repay another £317,000 because it attracted fewer pupils than expected in 2013-14.
Unlike most new academies, its funding is based on estimated pupil numbers, rather than it receiving their funding after its roll is confirmed.
The accounts note that: 'The academy is in discussions with the Education Funding Agency to agree a repayment plan that provides a sustainable solution for the academy and has been assured that sufficient cash will be made available to support the academy in the meantime.'
In the same year, the school's supply teacher costs almost doubled, from £92,000 to £183,000, which the school blamed on having 'a number of staff on long-term sick leave'.
The school is sponsored by the Transforming Education in Norfolk (TEN) group, which also includes City College Norwich, Fakenham, Attleborough and Wayland academies, and Norfolk's first university technical college.
In 2013, 24pc of pupils achieved five GCSEs at A*-C, including English and maths - a figure that rose to 29pc in 2014. The government's minimum floor standard is 40pc.
In his introduction to City Academy's accounts, Dick Palmer, chairman of governors and chief executive of the TEN Group, said its 2013 GCSE results 'did not meet our aspirational targets' and noted it had received a 'pre-warning notice' from the Department for Education.
His statement also revealed an Academy Improvement Board, chaired by the headmaster of the private Norwich School - who is a governor of City Academy - had been set up to 'monitor and the lead the implementation of a vigorous improvement plan aimed at addressing academic performance issues'.
In a separate set of accounts for the TEN Group's other academies, Mr Palmer said 'future growth plans have been put on hold whilst the group resolves performance issues elsewhere'.
A spokesman said: 'The TEN Group as a whole are determined that they must 'fix their own roof first'. This means that, while there is a dedication within the group to raising standards and results overall, there is special attention being paid to City Academy Norwich and a number of dedicated initiatives that use the power of combined resources and expertise within the group.'
He added: 'In a time of rapidly declining roll across Norfolk, City Academy Norwich recruited extremely well against its pre-16 capacity and we expect a similar picture for September 2015.
'The council's estimation of population growth and make-up in City Academy's catchment, unlike many others, predicts steady growth over the next ten years. We are confident that, with a new and dynamic principal [Mary Sparrow] in post and with the support its TEN Group partners, City Academy will be going from strength to strength.'
Do you have an education story? Email martin.george@archant.co.uk
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