Michael Gove has said schools are becoming one of the main sources of stability for children growing up in broken and struggling households.
The Education Secretary said at a Church of England seminar that increasing numbers of children in Britain today are "leading chaotic lives".
He said: "More and more children are growing up in homes where the male authority figure will be fleeting or absent, where there will be what we now call 'guesting' parents, and where many parents are struggling with mental health problems or substance abuse.
"And while it is very far from being a majority of parents, manifestly it is a growing and troubling minority and often concentrated in particular areas."
Gove said children turning up at school without breakfast was not because their families could not afford to provide it but because family life was "chaotic".
Gove spoke of households where children do not have a set bedtime or mealtime, and live "not knowing where mum or dad is at a particular time".
He suggested schools were one of the few places where children could learn the discipline, manners and punctuality that they are not being taught by their parents at home.
"That's why I think school can play a role in providing stability in those children's lives," he said.
The Education and Our Future seminar was hosted at Lambeth Palace by the Archbishop of Canterbury, the Most Reverend Justin Welby.
Concerns were raised during the seminar about the status and quality of Religious Education in schools after it was left out of the English Baccalaureate.
Gove said the decision had been made to address a shortage of mathematicians and scientists, and out of the belief that RE had "protection enough" as a compulsory subject.
He said he was "very anxious" to work with the Church of England and others to improve the quality of RE and "to celebrate great RE teaching".
The Education Secretary praised the role of the Church of England in educating the nation and encouraged it to be "optimistic" instead of "defensive" about changes in the education system, and "play a more energetic role".
The Archbishop of Canterbury said: "It is obviously true that good schools help produce an educated workforce. But the Christian vision is a far greater one. It is about setting a framework for children as they learn, which enables them to be confident when faced with the vast challenges that our rapidly changing culture brings to us."
The Bishop of Oxford, the Right Reverend John Pritchard, Chair of the Board of Education and National Society, said: "I was delighted to hear the Secretary of State's enthusiasm and admiration for church schools today. He reminded us that his own two children attend one of our schools and he applauded the Church for being prepared to work in places where others fear to tread.
"At the same time he set us a challenge to raise our game. This echoes our own determination to make a real step change in the way we serve our communities, working to the highest standards.
"I was also pleased to hear his public commitment to re-opening the conversation with the Churches on the future of RE and his recognition of its importance within the curriculum."