Charles Clarke, who was in the post from 2002 until 2004 has called on the government to change the rules in England and Wales to stop compulsory daily acts of collective worship.
Mr Clarke and Linda Woodhead, Professor of Religion and Philosophy at Lancaster University, have called for radical reform in England and Wales.
The British Humanist Association has welcomed this call to end compulsory worship and for a new national curriculum for education about religious and non-religious beliefs.
The pair argue the current relationship between faith and schools is out of date and want to abolish the requirement for all schools to hold daily worship with the government allowing more practical use of the time.
They have created a pamphlet setting out a series of recommendations including; replacing the RE syllabus that includes both religious and non-religious beliefs.
They stress that a religious and faith syllabus should be created on a national level and raise an issue with faith schools religiously discriminating in their admissions criteria.
Mr Clarke added that schools should hold daily acts of collective worship formed of a "broadly Christian character" and parents should be able to choose if they want to withdraw their children.
He argued that the era of daily worship is a "long gone" idea.
The Church of England released a statement by Revd Nigel Genders, Chief Education Officer. It reads:
"The Church of England continues to be committed to the provision of high quality RE in schools which is vital for a balanced understanding of the world today where more than 80% of the population are people of faith.
The Church strongly supports the statutory requirement for collective worship in all schools and there is plenty of flexibility in the provision to enable all pupils to benefit without compromising their faith or lack of it.
Where there are real objections it is a parent's right to withdraw their child from worship, and the very few who take up that right demonstrates that schools have found exciting and creative ways of using collective worship to further children's spiritual and moral development.
There is no expectation of commitment and the exposure to the range of religious traditions encourages community cohesion."
Revd Gavin Calver, Director for Mission at the Evangelical Alliance, told Premier's News Hour: "I think they'd be a real shame to the richness of our society.
"I think you look at somewhere like America where the education system is totally secularised and I think young people grow up in a slightly impoverished way as a result."
He added that the quality of the worship sessions needs to be addressed: "Some of this comes down to the ability to deliver, and if you look at the investment in teacher training and stuff in the delivery of anything to do with religious education - it's so low!"
Listen to Premier's Antony Bushfield speak to Revd Gavin Calver, Director for Mission at the Evangelical Alliance, here: