Children attending schools reconstructed under the flagship Building Schools for the Future scheme actually made less progress than children in similar state secondaries, it was disclosed.
Researchers also found that attendance was no better at the schools, despite huge investment in new classrooms, science labs, drama studios and sports facilities.
The disclosure follows a controversial decision by the Coalition to axe the programme which was set up by the former Government to rebuild every secondary school in England within the next 20 years.
The move prompted outrage among teachers, backbench MPs and local councils.
This week, it emerged that three local authorities – Nottingham, Luton and Waltham Forest in London – had launched legal action to reverse the decision.
Waltham Forest Council said attempts to pull funding would have a "catastrophic effect" on pupils.
But the latest study by the National Foundation for Educational Research suggests that benefits attached to new buildings may be overstated.
The small-scale study looked at the attendance and exam results of pupils at 60 BSF schools compared with similar students elsewhere.
Researchers took account of a range of factors including pupils’ background, gender, ethnicity, school type and eligibility for free meals.
“In all cases our models showed that pupils at BSF schools make, on average, less progress than would be expected based on their in-take and past performance,” said the report.
The findings show that these children achieved total a GCSE points score that was, on average, 11 points lower than that achieved by other pupils. This was equivalent to a drop of almost two grades.
The study found no significant difference in absence rates between pupils aged 14 to 16 in rebuilt schools and other state secondaries.
Ben Durbin, one of the report’s authors, said: "There has been a lot of controversy and conjecture about the benefits of new schools and this independent research, based on Government data, provides some hard facts.
"However, this study is based on a relatively limited dataset, and its findings should be considered in this context. We hope to carry out further work looking at more data."
Some 180 schools have been revamped since the programme was launched in 2004.
Axing the scheme in July, the Coalition said 700 new buildings would proceed as planned but plans for another 715 would be scrapped. --By Graeme Paton,05 Oct 2010