The Archbishop of Canterbury Justin Welby has been criticised for defending faith schools when they "prioritise evangelisation", according to a secular campaign group.
The Most Rev Welby defended faith schools, saying they are often in the poorest parts of the country.
But the National Secular Society (NSS) said Church of England schools "prioritise evangelisation over serving the population who are steadily abandoning his pews".
Asked about Birmingham City Council's inquiry into an alleged plot by Muslim hard-liners to seize control of governing bodies, the Archbishop told the BBC: "I can't talk about other faith schools, but it isn't much of a danger in Church of England schools."
The Trojan Horse allegations first came to light earlier this year, contained in an anonymous and unsigned letter, and have prompted separate on-going investigations by both the Department for Education and Ofsted.
Keith Porteous Wood, NSS executive director, said: "The Archbishop has jumped on the Birmingham Trojan Horse plot bandwagon to plug his Church's schools.
"The fundamentalism found in some minority schools is not seen in the Church's schools, as he says, but his Church is also banging the religious drum as hard as it can.
"He fails to point out that his schools, run entirely at public expense, prioritise evangelisation over serving the population who are steadily abandoning his pews."
The Most Rev Justin Welby reiterated his view that the UK is "a deeply Christian country".
But Mr Porteous Wood said this is a "self-serving claim" adding that Sunday church attendance has declined.
He said: "The Church's Establishment is often used as a justification by those claiming this is 'a deeply Christian country'.
"But Establishment, which Archbishop Welby is understandably so keen to retain, is an anachronism which these statistics of decline show the CofE has no justification or entitlement to.
"The UK should abandon the dwindling group of countries with established churches."
The Archbishop told the BBC that Church of England schools continued to "love and serve" as they "have done for hundreds of years".
Archbishop Welby also defended the role of faith schools within the education system, saying they remained "a very good use of social capital".
He said: "The way it's done with Church of England schools is that it's an expression of our love and service to the community.
"People seem to choose these schools in large numbers. They are often in the poorest parts of the country. We seek to love and serve people, as we should, through these schools - and have done for hundreds of years."
The Archbishop also said Christian faith was reflected in the "whole way we approach our national life".
He said the UK's "systems of justice and health, the way we value people, the basic way we look at the human being and the dignity of the human being, reflects the values of Jesus Christ".
He added: "We are a deeply Christian country in that way."