Grant-maintained schools have been accused of cherry-picking their pupils and discriminating against those from poor backgrounds and with special educational needs.
Opted-out schools also have fewer children from ethnic minorities and pupils who speak English as a second language, a study from the London Research Centre claims.
Grant-maintained schools have described the findings as "predictable", however, and branded the LRC as an "educational dinosaur".
The study shows that half of inner-London children attending LEA schools are entitled to free school meals, compared with 28 per cent in opted-out schools. In outer London, the figures were 25 per cent and 15 per cent respectively.
A third of youngsters in LEA schools speak a first language other than English while the same is true of only 9 per cent of those attending GM schools.
The figures also show that council-run schools take in 45 per cent of children from ethnic backgrounds compared with 38 per cent in GM schools.
Anne Page, chief executive of the LRC, an information service funded by the 33 London boroughs, said: "These figures starkly demonstrate that social selection, whether intended or not, is operating throughout the grant-maintained school sector.
"These figures demonstrate that GM schools are recruiting fewer children from poor families, fewer children known to have special educational needs and fewer children for whom English is not a first language.
"All such pupils need more teaching and other resources to redress these factors, known to affect their educational achievement. Politicians and policy-makers will need to act on these findings."
The study also shows that almost twice as many special needs children are attending local authority schools as attend opted-out schools - 2.7 per cent compared with 1.5 per cent.
Adrian Pritchard, director of the Grant Maintained Schools Foundation, said: "This is a predictable report compiled by the education dinosaur. It is parents who make the choice of where to send their children and not the schools hand-picking which pupils they want."
George Phipson, head of West Hatch High School in Essex and chairman of the Association of Heads of GM School, said the LRC findings were open to debate.
"Many schools opted out precisely because they wished to retain a comprehensive intake when something else was being foisted upon them.
"There are no grounds for believing that GM schools are operating covert methods to keep out certain children."
The LRC study also revealed that 2,000 children from a total pupil population of more than one million were excluded in the past year.