The criticism comes only months after the National College of School Leadership launched a slim-line modular version of the National Professional Qualification for Headteachers. Lord Dearing's report on church schools said no element of the qualification specifically dealt with church schools.
Lord Dearing, who has been dubbed education's "Mr Fix-it", urged the Church of England to take the matter up with the college.
Canon John Hall, general secretary of the C of E Board of Education, said there had been discussions with the college about the role of church school heads as spiritual leaders.
He said: "The headship of a church school is essentially the leadership of a Christian community - and that does mean something that's a bit different from the headship of a community school."
Heather du Quesnay, the college's chief executive, said: "Te (NPQH) qualification has been designed to deal with generic leadership skills rather than meet the needs of specific kinds of schools - there is no distinction between primary and secondary.
"However the qualification has just been reviewed and both the college and the profession would like to see those changes properly bedded down before any more are made.
"We are in discussion with both the Church of England and the Roman Catholic Church about how the college can better meet the needs of leaders in church schools."
Many church schools find it harder to recruit leaders because they generally insist on heads being committed Christians. Church schools are also worried that not enough fast-track places for high-flying trainees are being provided by church institutions.
* Applications for headship training are down from 3,000 in November to 2,300 this month. Despite the fall, the college said it was pleased with the figures as recruitment rounds are now held every six months rather than annually.