A total of 59 church schools are in the top 100 primary schools. Thirty-two are voluntary-aided; 27 voluntary-contro lled; 37 county and four grant-maintained.
The figures are significant because, of the total of 14,488 schools of all types in the performance league tables, only 3,204 are voluntary-aided and 2,193 voluntary-controlled. The total number of grant-maintained primaries in the tables is 421.
Education and Employment Secretary Gillian Shephard claimed as many as 71 of the best performers were GM or church schools. and insisted the tables showed that GM and church schools achieved excellence.
The majority of headteachers of voluntary-aided and voluntary-controlled schools contacted by The TES attributed church schools' success to small classes and a caring, sharing ethos.
Many Church of England schools are in small rural settings which do not have the same problems as the inner cities.
But Margaret Smart, director of the Catholic Education Service, most of whose schools are in urban areas, said: "It is perhaps interesting to put this alongside evidence from the Office for Standards in Education where church schools come out top.
"Our schools are an integral part of the community, so it is not just pupils and teachers, it is parents and governors, and - particularly in primary schools - local parishes all working together with a common purpose and shared values. There is a unity about the whole thing. " But she warned that league tables merely showed the result of a single test on a single day, and that some of the schools at the bottom of the tables were doing "extraordinarily well".
A spokesman for the General Synod thought the strong Christian ethos of Church of England schools and the extra level of support from the diocese, as well as from local education authorities and parents, helped achievement and staff morale.
Barbara Taylor, the headteacher of Longney Church of England-controlled school, in Gloucester, which came 36th in the top 100, said: "Church of England schools tend to be in rural areas with perceivably better catchment areas, whereas the majority of county primaries tend to be in the towns and suburbs. There are not quite as many problems in the rural areas."
Mrs Taylor also noted the family atmosphere of village schools - she is on first-name terms with nearly all her pupils' parents. As there is often more than one age group in a class in small schools, the older children would look after the younger ones.
There was also less of a gender divide in village schools, she said. The boys-versus-girls culture she had encountered in a Sheffield inner-city school did not exist at Longney.
Andrea Ives, the headteacher of Birstwith Church of England-controlled school in Harrogate, North Yorkshire, which came 32nd in the performance table, described her small school as being like "an extended family".
Mike Cooke, head of Sissinghurst Church of England-aided school in Cranbrook, Kent, which came 42nd, said: "In both religious education and assembly we do the teaching of Jesus Christ and a little of this rubs off on the children. Duty and responsibility to others comes into their work in the curriculum."
At St Peter and St Paul Roman Catholic-aided school in Lichfield, Staffordshire, which came 27th in the table, headteacher Mark Fowler said on the issue of faith: "We value things which might not be so important in other schools. We value sharing and working together as a team very highly."