An independent evaluation into Tony Blair's flagship city academies scheme delivered a mixed verdict on their success yesterday.
Improvements in exam results at academies were better than at other comparable schools in England, "although the absolute differences are generally small".
And results have "actually deteriorated" at some of the academies, the report from accountants PricewaterhouseCoopers found.
Poor pupil behaviour and the design of the high-tech new buildings were also concerns.
The report, commissioned by the Department for Education and Skills, said it was too early to provide a definitive assessment of the overall success of the £5 billion initiative.
But the study highlighted the mixed exam results at the academies, which were set up in an attempt to transform failing comprehensives.
PwC said: "There is a clear diversity in pupil performance both between and within academies, and this is one of the most important findings to emerge from the research to date.
"In some academies, and depending on the indicator used, performance is actually deteriorating.
"In other academies, performance is improving in all subject areas, and in others, performance is improving in one subject and deteriorating in another."
Truancy levels and poor pupil behaviour were also problems for academies, the report found.
Significantly more pupils were expelled or suspended from academies than other schools for bad behaviour.
And rates of unauthorised absence, or truancy, rose twice as much in academies as the average rise across all schools in England between 2002 and 2004.
The Prime Minister introduced the academies programme in an attempt to transform failing comprehensives in some of the most deprived parts of the country.
In exchange for up to £2 million, private sponsors receive a major say in the running of a new academy, including setting the school's ethos and appointing governors.
The rest of the start-up costs - typically around £25 million - are met by Government funds.
Birmingham City Council has been given the go ahead to create seven city academies backed by the private sector.
But the seven schools will offer something different to the Government's model, having more than one sponsor to dispel fears of one individual or organisation gaining undue influence over pupils. Also some of the schools may be refurbished.
In the face of criticism that the scheme is too expensive, Ministers have insisted that academies cost no more than other state schools.
The injection of extra funding - for buildings and computer equipment - was a major factor in "promoting a more positive environment".
But the evaluation raised concerns about some of the new buildings, with "ongoing issues" in relation to the extent to which the new buildings are fit for purpose.