Of the 112 secondaries praised for their excellence following inspection visits in 1999-2000, 24 are supported either by the Church of England or the Roman Catholics. Nationally, only one in eight secondaries is a church school.
In the primary sector, church schools were under-represented - at 28 per cent of those praised. Nationally, 35 per cent of primaries are church schools.
An Office for Standards in Education spokesman said that church schools were helped by the fact that parents and pupils often had a strong commitment to the values and ethos of th school.
He added: "Even if schools are selecting purely on religious grounds, they are attracting pupils who are likely to come from supportive backgrounds and be better behaved."
He added that less selection and more inclusion at primary level could explain why church schools did not dominate the primary list.
Mr Tomlinson said that primaries serving disadvantaged areas were improving at faster-than-average rates.
They were also over-represented on the list of the most successful schools, with half of those on the list having at least a fifth of their pupils on free meals.
But this was not the case at secondary level, where the gap between the most and least effective schools was growing.