Headteachers have been told consultation does not mean parents have the right to veto parts of the new relationships and sex education curriculum.
It comes as mostly Muslim parents have held protests outside Birmingham's Parkfield Community School against their children being taught about same sex relationships.
In a letter to the National Association for Head Teachers (NAHT), education secretary Damian Hinds said consulting parents does not allow them to dismiss what they do not want their children learning.
He also said a core part of preparing children for life in modern Britain is ensuring they understand the world they are growing up in.
Writing to NAHT general secretary Paul Whiteman, he said: "Head teachers across the country do a fantastic job of leading their schools, and I want to make sure that they, as the people who best know their pupils and communities, are supported to do their jobs."
Speaking to talkRADIO's Julia Hartley-Brewer, the education secretary said the Equality Act ensured the public sector was "respectful and inclusive of all people” and that religious faith was a protected characteristic.
“It is good to talk and dialogue about these things is important," he said. "Parents are the prime educators of their children in many ways.
“There is not a hierarchy in the Equality Act between the different protected characteristics ... it is about respect and that starts with being able to talk valuing people being different and how together that makes us a stronger society.”
Julia resopnded by questioning whether the views of people who "think that gay people should go to prison for being gay" should be respected.
Mr Hinds accused Julia of “putting words” in his mouth, adding: “at no point did I say that I respected those views or anything like them," adding it was important children “know there are different types of families” and can learn about it in “a safe and supportive environment”.
From 2020, three new subjects - relationships education from primary school, relationships and sex education at secondary school, and health education for all ages - will form part of the school curriculum in England.
Mr Hinds said: “There is also a distinction between sex and relationship education. Primary schools are not required to do sex education but they will be required to do relationship education in the future.
“If they do also do sex education then parents have the right to withdraw their children. That is a long-standing right that I will defend.”