City academies are proving broadly popular with parents, but are facing a number of "significant" problems, a report commissioned by ministers says.
City academies are housed in new buildings
It found 66% of 433 parents thought private sponsorship of up to £2m had "made a difference" at their school.
But it said bullying was still a problem in some academies.
The government wants 200 academies - which replace failing urban schools at an average cost of £25m each - in place or under construction by 2010.
The report, carried out by PricewaterhouseCoopers (PwC), pointed to a series of "not insignificant challenges" faced by those already up and running.
Academies, which are independently-run, state-funded schools, needed to learn how to achieve a "balance between new and existing staff".
There was a "lack of clarity" over admissions of children with special educational needs, it said.
Under the academies scheme, failing schools are demolished and replaced with "state-of-the-art" buildings.
Private sponsors - usually businesses, charities or wealthy individuals - put in up to £2m, with the remaining start-up costs paid by government.
Sponsors choose the majority of governors.
Heads 'really good'
Critics say this gives them undue influence over children's education, but the survey found that 55% of staff thought sponsors' resources had helped learning, with just 12% disagreeing.
Some 68% of pupils felt academies' head teachers were "really good". However, 10% did not even know who was doing the job.
When it came to the new buildings, 60% of pupils said they made "a difference", while 74% of parents said they helped learning.
Education Secretary Ruth Kelly said: "The report demonstrates the real progress that the first academies have begun to make in turning around the life chances of thousands of children in the most deprived areas of the country.
"There is much more to do. But we have a sound basis on which to build."
In March, the Commons education select committee said academy funding should be withheld until the programme was shown to be cost-effective.
So far, 17 academies have been set up. PwC's survey was carried out at the beginning of last year, less than a year-and-a-half after the first ones had opened.
PwC received responses from 1,666 pupils and 403 teachers.
It said the findings - based on 10 academies - should be treated as "preliminary, indicative and subject to further refinement".
Rona Kiley, chief executive of the Academy Sponsors Trust, said: "There has been much controversy over academies based largely on anecdotes, but this report provides important early evidence."
Steve Sinnott, general secretary of the National Union of Teachers, said: "There is nothing surprising in the finding that pupils and parents support their new schools.
"The same would be the result if parents and pupils of any new school were asked the same questions."
'Controversy should end'
But the leader of the National Association of Head Teachers, David Hart, said: there was "every evidence" most academies were doing a better job than
the schools they had replaced, but they were "burdened with excessive expectations".
"It takes time to turn round a failing school," he said.
"The political dogma and controversy that has surrounded academies should
The Advisory Centre for Education, a help group for parents, said the report noted greater use of exclusions than was usual nationally.
It was concerned there were not effective checks on whether academies might be using exclusion - as well as admissions - to select pupils, given that they were supposed to be serving disadvantaged sectors of the population.