Academies in England are improving pupils' exam performances but the benefits are "not universal", a survey for the government suggests.
City academies involve a complete rebuilding of premises
In most of the 15 academies looked at, children were getting better at tests at age 14 and in GCSEs.
But in some, performances were "actually deteriorating", PricewaterhouseCoopers found.
Education Secretary Alan Johnson said there was "growing evidence" of achievement but also "more to do".
The report said it was too early to provide a full assessment of the £5bn academies initiative, aimed at raising achievement in deprived areas.
It added: "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."
The government has set a target of having 200 city academies open or under construction by 2010. So far, 27 have opened.
Under the scheme, private sponsors provide up to £2m towards start-up costs, giving them a say in the academy's running.
Old schools are demolished and rebuilt, typically at a cost of about £25m.
The report said there were "ongoing issues in relation to the extent to which the new buildings are fit for purpose.
"There is also some evidence to suggest that managing pupils' behaviour remains a challenge for some academies."
Steve Sinnott, general secretary of the National Union of Teachers, said: "The government's creation of a group of institutions that are funded more generously and which are isolating themselves from other schools is leading to a divided and fragmented education service.
"This will not promote social cohesion nor will the government live up to its claim that every child matters."
But Mr Johnson said: "Academies serve deprived areas with a history of poorly performing schools which past strategies failed to turn around.
"In contrast in only a few years academies have brought a new ethos of success and created schools parents want to send their children to."
Shadow Schools Minister Nick Gibb said: "We strongly support the academies programme and are pleased that once again research shows they are achieving better results than the schools they replaced."