A study by the Institute for Research in Integrated Strategies shows that Anglican and Catholic schools in central London, where competition for places is the fiercest, have an average of two fewer children from low-income families in every class.
The findings appear to contradict claims by Dr Rowan Williams, the Archbishop of Canterbury, that faith schools do not cherry-pick pupils.
The report analysed the admissions arrangements of the 17,319 primary schools in England, focusing on voluntary-aided Anglican and Catholic schools in urban and rural areas.
It found that almost 22 per cent of children in the postcode areas of urban Anglican primaries were eligible for free meals - the Government's key indicator of social deprivation - but only 18.8 per cent attended the school.
Similarly, more than 27 per cent of children living within the catchment areas of urban Catholic primaries were eligible for free meals, but only 18.9 per cent attended those schools.
In comparison, non-religious primaries accepted more than their share of deprived children. The study showed that, on average, 24.5 per cent of children living within the postcode areas of urban primaries were said to be from low-income families, but 26.5 per cent of their pupils were actually on free meals.
Similar patterns were found in primaries in rural communities.
Chris Waterman, the report's author and chief executive of Confed, which represents local authority directors, said inner-city London schools were worst affected.
More than 41 per cent of children living near Anglican primaries in the capital were eligible for free meals, but just 32 per cent went to such schools.
Almost 42 per cent lived near Catholic primaries but only 28.3 per cent attended those schools. In comparison, non-religious schools admitted more children on free meals than were actually living in the local area.
Mr Waterman said: "Across inner London, church primary schools have some 12,000 fewer pupils with free meals than non-religious schools - that equates to about two children per class.
"It is clear that there are unexplained factors at work, which mean fewer children from deprived backgrounds attend church primaries in comparison to other schools."
The report follows earlier figures, published by the Department for Education and Skills, which show fewer children with special needs attend faith-based schools than community schools.
Dr Williams said in a speech last week that faith schools did not favour middle-class families, but added that Anglican primaries and secondaries should adopt national standards for admissions.
Canon John Hall, the C of E's chief education officer, said it was hard to generalise about church school admissions, adding: "If there was covert social selection for church schools - of which there is no actual evidence - we would deplore it and seek to root it out."